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Sample records for diverse populations significant

  1. Diversity of Poissonian populations.

    Science.gov (United States)

    Eliazar, Iddo I; Sokolov, Igor M

    2010-01-01

    Populations represented by collections of points scattered randomly on the real line are ubiquitous in science and engineering. The statistical modeling of such populations leads naturally to Poissonian populations-Poisson processes on the real line with a distinguished maximal point. Poissonian populations are infinite objects underlying key issues in statistical physics, probability theory, and random fractals. Due to their infiniteness, measuring the diversity of Poissonian populations depends on the lower-bound cut-off applied. This research characterizes the classes of Poissonian populations whose diversities are invariant with respect to the cut-off level applied and establishes an elemental connection between these classes and extreme-value theory. The measures of diversity considered are variance and dispersion, Simpson's index and inverse participation ratio, Shannon's entropy and Rényi's entropy, and Gini's index.

  2. Warfarin Pharmacogenomics in Diverse Populations.

    Science.gov (United States)

    Kaye, Justin B; Schultz, Lauren E; Steiner, Heidi E; Kittles, Rick A; Cavallari, Larisa H; Karnes, Jason H

    2017-09-01

    Genotype-guided warfarin dosing algorithms are a rational approach to optimize warfarin dosing and potentially reduce adverse drug events. Diverse populations, such as African Americans and Latinos, have greater variability in warfarin dose requirements and are at greater risk for experiencing warfarin-related adverse events compared with individuals of European ancestry. Although these data suggest that patients of diverse populations may benefit from improved warfarin dose estimation, the vast majority of literature on genotype-guided warfarin dosing, including data from prospective randomized trials, is in populations of European ancestry. Despite differing frequencies of variants by race/ethnicity, most evidence in diverse populations evaluates variants that are most common in populations of European ancestry. Algorithms that do not include variants important across race/ethnic groups are unlikely to benefit diverse populations. In some race/ethnic groups, development of race-specific or admixture-based algorithms may facilitate improved genotype-guided warfarin dosing algorithms above and beyond that seen in individuals of European ancestry. These observations should be considered in the interpretation of literature evaluating the clinical utility of genotype-guided warfarin dosing. Careful consideration of race/ethnicity and additional evidence focused on improving warfarin dosing algorithms across race/ethnic groups will be necessary for successful clinical implementation of warfarin pharmacogenomics. The evidence for warfarin pharmacogenomics has a broad significance for pharmacogenomic testing, emphasizing the consideration of race/ethnicity in discovery of gene-drug pairs and development of clinical recommendations for pharmacogenetic testing. © 2017 Pharmacotherapy Publications, Inc.

  3. Noonan syndrome in diverse populations.

    Science.gov (United States)

    Kruszka, Paul; Porras, Antonio R; Addissie, Yonit A; Moresco, Angélica; Medrano, Sofia; Mok, Gary T K; Leung, Gordon K C; Tekendo-Ngongang, Cedrik; Uwineza, Annette; Thong, Meow-Keong; Muthukumarasamy, Premala; Honey, Engela; Ekure, Ekanem N; Sokunbi, Ogochukwu J; Kalu, Nnenna; Jones, Kelly L; Kaplan, Julie D; Abdul-Rahman, Omar A; Vincent, Lisa M; Love, Amber; Belhassan, Khadija; Ouldim, Karim; El Bouchikhi, Ihssane; Shukla, Anju; Girisha, Katta M; Patil, Siddaramappa J; Sirisena, Nirmala D; Dissanayake, Vajira H W; Paththinige, C Sampath; Mishra, Rupesh; Klein-Zighelboim, Eva; Gallardo Jugo, Bertha E; Chávez Pastor, Miguel; Abarca-Barriga, Hugo H; Skinner, Steven A; Prijoles, Eloise J; Badoe, Eben; Gill, Ashleigh D; Shotelersuk, Vorasuk; Smpokou, Patroula; Kisling, Monisha S; Ferreira, Carlos R; Mutesa, Leon; Megarbane, Andre; Kline, Antonie D; Kimball, Amy; Okello, Emmy; Lwabi, Peter; Aliku, Twalib; Tenywa, Emmanuel; Boonchooduang, Nonglak; Tanpaiboon, Pranoot; Richieri-Costa, Antonio; Wonkam, Ambroise; Chung, Brian H Y; Stevenson, Roger E; Summar, Marshall; Mandal, Kausik; Phadke, Shubha R; Obregon, María G; Linguraru, Marius G; Muenke, Maximilian

    2017-09-01

    Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world. © 2017 Wiley Periodicals, Inc.

  4. Genetic Diversity and Population Structure of the Pelagic Thresher Shark (Alopias pelagicus) in the Pacific Ocean: Evidence for Two Evolutionarily Significant Units

    Science.gov (United States)

    Cardeñosa, Diego; Hyde, John; Caballero, Susana

    2014-01-01

    There has been an increasing concern about shark overexploitation in the last decade, especially for open ocean shark species, where there is a paucity of data about their life histories and population dynamics. Little is known regarding the population structure of the pelagic thresher shark, Alopias pelagicus. Though an earlier study using mtDNA control region data, showed evidence for differences between eastern and western Pacific populations, the study was hampered by low sample size and sparse geographic coverage, particularly a lack of samples from the central Pacific. Here, we present the population structure of Alopias pelagicus analyzing 351 samples from six different locations across the Pacific Ocean. Using data from mitochondrial DNA COI sequences and seven microsatellite loci we found evidence of strong population differentiation between western and eastern Pacific populations and evidence for reciprocally monophyly for organelle haplotypes and significant divergence of allele frequencies at nuclear loci, suggesting the existence of two Evolutionarily Significant Units (ESU) in the Pacific Ocean. Interestingly, the population in Hawaii appears to be composed of both ESUs in what seems to be clear sympatry with reproductive isolation. These results may indicate the existence of a new cryptic species in the Pacific Ocean. The presence of these distinct ESUs highlights the need for revised management plans for this highly exploited shark throughout its range. PMID:25337814

  5. Population genetic diversity and fitness in multiple environments

    Directory of Open Access Journals (Sweden)

    McGreevy Thomas J

    2010-07-01

    Full Text Available Abstract Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater and stressful conditions (diluted seawater. The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation

  6. Genetic diversity of endangered populations of Butia capitata ...

    African Journals Online (AJOL)

    The flora and fauna of the Cerrado biome in central Brazil both show great diversity and high levels of endemism. Butia capitata is a palm native to this biome that has significant economic, social, and environmental value. We sought to identify and quantify the genetic diversity of four fragmented populations of B. capitata ...

  7. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

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    Jiali Zhao

    Full Text Available We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China.We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China.We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

  8. Career Development of Diverse Populations. ERIC Digest.

    Science.gov (United States)

    Kerka, Sandra

    Career development theories and approaches have been criticized for lack of applicability to diverse populations. Traditional career development theories and models assume that: everyone has a free choice among careers; career development is a linear, progressive, rational process; and individualism, autonomy and centrality of work are universal…

  9. Significant population of Egyptian Vulture Neophron percnopterus ...

    African Journals Online (AJOL)

    The Egyptian Vulture Neophron percnopterus population in Morocco has undergone a marked decline since the 1980s to the point of nearing local extinction in the twenty-first century. A field study of some possible sites for Egyptian Vultures was carried out over six days during June 2014 in the Middle Atlas Mountains, ...

  10. Raw Sewage Harbors Diverse Viral Populations

    Science.gov (United States)

    Cantalupo, Paul G.; Calgua, Byron; Zhao, Guoyan; Hundesa, Ayalkibet; Wier, Adam D.; Katz, Josh P.; Grabe, Michael; Hendrix, Roger W.; Girones, Rosina; Wang, David; Pipas, James M.

    2011-01-01

    ABSTRACT At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity. Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that

  11. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Science.gov (United States)

    Melito, Sara; Sias, Angela; Petretto, Giacomo L; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

  12. Genetic and metabolite diversity of Sardinian populations of Helichrysum italicum.

    Directory of Open Access Journals (Sweden)

    Sara Melito

    Full Text Available BACKGROUND: Helichrysum italicum (Asteraceae is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. METHODS: H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. KEY RESULTS: The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. CONCLUSIONS: The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil.

  13. Diverse Populations in Saskatchewan: The Challenges of Reaching Them

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    Maha Kumaran

    2010-07-01

    Full Text Available Saskatchewan is more diverse than it was even 5 years ago. Although historically Saskatchewan has always had a diverse immigrant population with new immigrants coming from many European and Eastern European countries, recently there are large immigrant communities arriving: some as refugees, some as guest workers, international students and their families from several parts of the globe through various significant government initiatives and policies. Not only is this diverse immigrant population growing, but the social make up of the new immigrants is also changing. There are many reasons why Saskatchewan is receiving more immigrants. This paper states those reasons, discusses the history of immigration in Saskatchewan, current immigrant situation, and the role libraries can play in educating, informing and entertaining these immigrant populations. This paper focuses on new immigrants coming into Saskatchewan and does not discuss other groups that are part of a diverse society such as aboriginal populations, seniors, the GBLT, or French Canadians. The authors sent out questionnaires to see what other libraries in Canada have done in this area and have looked into Vancouver Public Library and Toronto Public Library as examples for programs and services that can be offered to diverse immigrant populations.

  14. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    , the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two...... the ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least...

  15. Germination rate is the significant characteristic determining coconut palm diversity

    Science.gov (United States)

    Harries, Hugh C.

    2012-01-01

    Rationale This review comes at a time when in vitro embryo culture techniques are being adopted for the safe exchange and cryo-conservation of coconut germplasm. In due course, laboratory procedures may replace the options that exist among standard commercial nursery germination techniques. These, in their turn, have supplanted traditional methods that are now forgotten or misunderstood. Knowledge of all germination options should help to ensure the safe regeneration of conserved material. Scope This review outlines the many options for commercial propagation, recognizes the full significance of one particular traditional method and suggests that the diversity of modern cultivated coconut varieties has arisen because natural selection and domestic selection were associated with different rates of germination and other morphologically recognizable phenotypic characteristics. The review takes into account both the recalcitrant and the viviparous nature of the coconut. The ripe fruits that fall but do not germinate immediately and lose viability if dried for storage are contrasted with the bunches of fruit retained in the crown of the palm that may, in certain circumstances, germinate to produce seedlings high above ground level. Significance Slow-germinating and quick-germinating coconuts have different patterns of distribution. The former predominate on tropical islands and coastlines that could be reached by floating when natural dispersal originally spread coconuts widely—but only where tides and currents were favourable—and then only to sea-level locations. Human settlers disseminated the domestic types even more widely—to otherwise inaccessible coastal sites not reached by floating—and particularly to inland and upland locations on large islands and continental land masses. This review suggests four regions where diversity has been determined by germination rates. Although recent DNA studies support these distinctions, further analyses of genetic markers

  16. Germination rate is the significant characteristic determining coconut palm diversity.

    Science.gov (United States)

    Harries, Hugh C

    2012-01-01

    This review comes at a time when in vitro embryo culture techniques are being adopted for the safe exchange and cryo-conservation of coconut germplasm. In due course, laboratory procedures may replace the options that exist among standard commercial nursery germination techniques. These, in their turn, have supplanted traditional methods that are now forgotten or misunderstood. Knowledge of all germination options should help to ensure the safe regeneration of conserved material. This review outlines the many options for commercial propagation, recognizes the full significance of one particular traditional method and suggests that the diversity of modern cultivated coconut varieties has arisen because natural selection and domestic selection were associated with different rates of germination and other morphologically recognizable phenotypic characteristics. The review takes into account both the recalcitrant and the viviparous nature of the coconut. The ripe fruits that fall but do not germinate immediately and lose viability if dried for storage are contrasted with the bunches of fruit retained in the crown of the palm that may, in certain circumstances, germinate to produce seedlings high above ground level. Slow-germinating and quick-germinating coconuts have different patterns of distribution. The former predominate on tropical islands and coastlines that could be reached by floating when natural dispersal originally spread coconuts widely-but only where tides and currents were favourable-and then only to sea-level locations. Human settlers disseminated the domestic types even more widely-to otherwise inaccessible coastal sites not reached by floating-and particularly to inland and upland locations on large islands and continental land masses. This review suggests four regions where diversity has been determined by germination rates. Although recent DNA studies support these distinctions, further analyses of genetic markers related to fruit abscission and

  17. Standard filtration practices may significantly distort planktonic microbial diversity estimates

    Directory of Open Access Journals (Sweden)

    Cory Cruz Padilla

    2015-06-01

    Full Text Available Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40-60% of prefilter datasets at low volumes (0.05-0.5 L to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold. Taxon richness (97% similarity clusters also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

  18. Diversity and population structure of red rice germplasm in Bangladesh.

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    M Z Islam

    Full Text Available While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35. While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V, a similar SSR analysis yielded only three major groups (I, II, and III, and a model-based population structure analysis yielded four (A, B, C and D. Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA, as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207 among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular

  19. Diversity and population structure of red rice germplasm in Bangladesh.

    Science.gov (United States)

    Islam, M Z; Khalequzzaman, M; Prince, M F R K; Siddique, M A; Rashid, E S M H; Ahmed, M S U; Pittendrigh, B R; Ali, M P

    2018-01-01

    While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

  20. Loss of genetic diversity in Maculinea populations over 10 years

    DEFF Research Database (Denmark)

    Nash, David Richard; Lomborg, Andreas Eg

    I will present the results of research on the population genetics of Maculinea alcon and M. arion in Southern scandinavia, which shows a strong decrease in genetic diversity in most populations, even if those populations are apparently otherwise healthy....

  1. Restoration of coral populations in light of genetic diversity estimates

    Science.gov (United States)

    Shearer, T. L.; Porto, I.; Zubillaga, A. L.

    2009-09-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species ( Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10-35 randomly selected local donor colonies will retain at least 50-90% of the genetic diversity of the original population.

  2. Analysis of iris surface features in populations of diverse ancestry

    Science.gov (United States)

    Edwards, Melissa; Cha, David; Krithika, S.; Johnson, Monique; Parra, Esteban J.

    2016-01-01

    There are many textural elements that can be found in the human eye, including Fuchs’ crypts, Wolfflin nodules, pigment spots, contraction furrows and conjunctival melanosis. Although iris surface features have been well-studied in populations of European ancestry, the worldwide distribution of these traits is poorly understood. In this paper, we develop a new method of characterizing iris features from photographs of the iris. We then apply this method to a diverse sample of East Asian, European and South Asian ancestry. All five iris features showed significant differences in frequency between the three populations, indicating that iris features are largely population dependent. Although none of the features were correlated with each other in the East and South Asian groups, Fuchs’ crypts were significantly correlated with contraction furrows and pigment spots and contraction furrows were significantly associated with pigment spots in the European group. The genetic marker SEMA3A rs10235789 was significantly associated with Fuchs’ crypt grade in the European, East Asian and South Asian samples and a borderline association between TRAF3IP1 rs3739070 and contraction furrow grade was found in the European sample. The study of iris surface features in diverse populations may provide valuable information of forensic, biomedical and ophthalmological interest. PMID:26909168

  3. Diversity Generation in Evolving Microbial Populations

    DEFF Research Database (Denmark)

    Markussen, Trine

    Pseudomonas aeruginosa infections in the airways of patients with cystic fibrosis (CF) offer opportunities to study bacterial evolution and adaptation in natural environments. Significantly phenotypic and genomic changes of P. aeruginosa have been observed during chronic infection. While P. aeruginosa...... bacterial genome sequencing, phenotypic profiling and unique sampling materials which included clonal bacterial isolates sampled for more than 4 decades from chronically infected CF patients, we were able to investigate the diversity generation of the clinical important and highly successful P. aeruginosa...... DK1 clone type during chronic airway infection in CF patients. We show here that diversification of P. aeruginosa DK1 occurs through the emergence of coexisting subpopulations with distinct phenotypic and genomic features and demonstrate that this diversification was a result of niche specialization...

  4. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for

  5. A population memetics approach to cultural evolution in chaffinch song: meme diversity within populations.

    Science.gov (United States)

    Lynch, A; Baker, A J

    1993-04-01

    We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, Canaries) and neighboring continental regions (Morocco, Iberia) by employing a population memetics approach. To quantify variability within populations, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The frequency distribution of memes within populations generally fit a neutral model in which there is an equilibrium between mutation, migration, and drift, which suggests that memes are functionally equivalent. The diversity of memes of single syllables is significantly greater in the Azores compared to all other regions, consistent with higher population densities of chaffinches there. On the other hand, memes of two to five syllables have greater diversity in Atlantic island and Moroccan populations compared to their Iberian counterparts. This higher diversity emanates from a looser syntax and increased recombination in songs, presumably because of relaxed selection for distinctive songs in these peripheral and depauperate avifaunas. We urge comparative population memetic studies of other species of songbirds and predict that they will lead to a formulation of a general theory for the cultural evolution of bird song analogous to population genetics theory for biological traits.

  6. Genetic diversity of disease-associated loci in Turkish population.

    Science.gov (United States)

    Karaca, Sefayet; Cesuroglu, Tomris; Karaca, Mehmet; Erge, Sema; Polimanti, Renato

    2015-04-01

    Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.

  7. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  8. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  9. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  10. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  11. Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

    Science.gov (United States)

    Hellmair, Michael; Kinziger, Andrew P

    2014-01-01

    Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

  12. Increased extinction potential of insular fish populations with reduced life history variation and low genetic diversity.

    Directory of Open Access Journals (Sweden)

    Michael Hellmair

    Full Text Available Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi, show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species.

  13. Mycorrhizal symbioses of Salix repens : diversity and functional significance

    NARCIS (Netherlands)

    Heijden, van der E.W.

    2000-01-01

    This thesis investigates the significance of different mycorrhizal fungi, belonging to different functional types (arbuscular mycorrhiza-AM and ectomycorrhiza-EcM), in Salix repens . A comparison between above-ground and below-ground observations on ectomycorrhizal

  14. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  15. Analysis of genetic diversity and population structure in upland ...

    Indian Academy of Sciences (India)

    Mulugeta Seyoum

    2018-06-09

    Jun 9, 2018 ... diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions ...... conservation of cotton germplasm in China (English abstract). ... and Alishah O. 2011 Inter simple sequence repeats (ISSR).

  16. Genetic diversity among natural populations of Ottelia acuminata ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... is essential for establishing effective and efficient conser- vation and breeding ... overlaid with 40 µl mineral oil. Amplifications were .... Diversity for Nineteen Populations of Pinus sibirica Du Tour with. Technique of ISSR.

  17. Time related total lactic acid bacteria population diversity and ...

    African Journals Online (AJOL)

    user

    2011-02-07

    Feb 7, 2011 ... the diversity and dynamics of lactic acid bacteria (LAB) population in fresh ..... combining morphological, biochemical and molecular data are important for ..... acid bacteria from fermented maize (Kenkey) and their interactions.

  18. Genetic diversity in coastal and inland desert populations of ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-14

    Nov 14, 2011 ... 0.00196 showed low degree of differentiation among populations. .... number of amplification products per primer varied from 6 to 14, and these ..... strategies on genetic diversity estimates obtained with RAPD markers in ...

  19. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... and other aquatic ecosystem and the ecological complexes. ... is a property at the population level while the functional diversity concept ... warm water fish species, which are distributed all over the world. ..... Phylogenetic.

  20. Similar levels of diversity and population Structure in superflock and ...

    African Journals Online (AJOL)

    superflock cichlid fishes from Lake Victoria, Africa. ... Tropical Freshwater Biology ... We use DNA microsatellite loci to estimate neutral genetic diversity and the level of gene flow among populations of two cichlid species from southern Lake Victoria, ...

  1. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  2. Great ape genetic diversity and population history

    DEFF Research Database (Denmark)

    Prado-Martinez, Javier; Sudmant, Peter H; Kidd, Jeffrey M

    2013-01-01

    Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape...

  3. Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides)

    Science.gov (United States)

    Colin M. Callahan; Carol A. Rowe; Ronald J. Ryel; John D. Shaw; Michael D. Madritch; Karen E. Mock

    2013-01-01

    Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the southwestern cluster may result from distinct gene pools separated during the Pleistocene...

  4. Evolutionary Dynamics and Diversity in Microbial Populations

    Science.gov (United States)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  5. Identification of diverse astrocyte populations and their malignant analogs.

    Science.gov (United States)

    John Lin, Chia-Ching; Yu, Kwanha; Hatcher, Asante; Huang, Teng-Wei; Lee, Hyun Kyoung; Carlson, Jeffrey; Weston, Matthew C; Chen, Fengju; Zhang, Yiqun; Zhu, Wenyi; Mohila, Carrie A; Ahmed, Nabil; Patel, Akash J; Arenkiel, Benjamin R; Noebels, Jeffrey L; Creighton, Chad J; Deneen, Benjamin

    2017-03-01

    Astrocytes are the most abundant cell type in the brain, where they perform a wide array of functions, yet the nature of their cellular heterogeneity and how it oversees these diverse roles remains shrouded in mystery. Using an intersectional fluorescence-activated cell sorting-based strategy, we identified five distinct astrocyte subpopulations present across three brain regions that show extensive molecular diversity. Application of this molecular insight toward function revealed that these populations differentially support synaptogenesis between neurons. We identified correlative populations in mouse and human glioma and found that the emergence of specific subpopulations during tumor progression corresponded with the onset of seizures and tumor invasion. In sum, we have identified subpopulations of astrocytes in the adult brain and their correlates in glioma that are endowed with diverse cellular, molecular and functional properties. These populations selectively contribute to synaptogenesis and tumor pathophysiology, providing a blueprint for understanding diverse astrocyte contributions to neurological disease.

  6. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  7. Noninvasive genetics provides insights into the population size and genetic diversity of an Amur tiger population in China.

    Science.gov (United States)

    Wang, Dan; Hu, Yibo; Ma, Tianxiao; Nie, Yonggang; Xie, Yan; Wei, Fuwen

    2016-01-01

    Understanding population size and genetic diversity is critical for effective conservation of endangered species. The Amur tiger (Panthera tigris altaica) is the largest felid and a flagship species for wildlife conservation. Due to habitat loss and human activities, available habitat and population size are continuously shrinking. However, little is known about the true population size and genetic diversity of wild tiger populations in China. In this study, we collected 55 fecal samples and 1 hair sample to investigate the population size and genetic diversity of wild Amur tigers in Hunchun National Nature Reserve, Jilin Province, China. From the samples, we determined that 23 fecal samples and 1 hair sample were from 7 Amur tigers: 2 males, 4 females and 1 individual of unknown sex. Interestingly, 2 fecal samples that were presumed to be from tigers were from Amur leopards, highlighting the significant advantages of noninvasive genetics over traditional methods in studying rare and elusive animals. Analyses from this sample suggested that the genetic diversity of wild Amur tigers is much lower than that of Bengal tigers, consistent with previous findings. Furthermore, the genetic diversity of this Hunchun population in China was lower than that of the adjoining subpopulation in southwest Primorye Russia, likely due to sampling bias. Considering the small population size and relatively low genetic diversity, it is urgent to protect this endangered local subpopulation in China. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  8. Genetic diversity analysis in the Hypericum perforatum populations ...

    African Journals Online (AJOL)

    Assessment of genetic variability among the Hypericum perforatum populations is critical to the development of effective conservation strategies in the Kashmir valley. To obtain accurate estimates of genetic diversity among and within populations of H. perforatum, inter-simple sequence repeats (ISSR) markers were used.

  9. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  10. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  11. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  12. Genetic diversity of populations of the dioecious Myrsine coriacea (Primulaceae in the Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Roberta Pena da Paschoa

    2018-04-01

    Full Text Available ABSTRACT Although a species’ sexual system may influence the genetic diversity of its populations in their natural environment, there have been few such studies involving indigenous species of the Atlantic Forest. Here we study Myrsine coriacea, a dioecious tree widely used in reforestation programs despite a lack of information about its natural interpopulation genetic variation. To address this knowledge gap, intra- and interpopulation genetic diversity were measured for male and female individuals of ten natural populations using ISSR markers. Greater intrapopulation genetic diversity indicated interpopulation gene flow, regardless of isolation and distance between populations. Multivariate analyses detected significant differences in genetic diversity between populations, but not between males and females, which indicates that genetic diversity did not differ between the two sex morphs. Distance between populations was unrelated to genetic diversity. Myrsine coriacea has not experienced a loss of genetic variability despite the characteristic segregated spatial distribution of its populations. These results suggest that obligatory cross-pollination and dispersal by birds may be important mechanisms for the maintenance of genetic diversity in natural populations of M. coriacea.

  13. Genetic Diversity in Natural Populations of New World Leishmania

    Directory of Open Access Journals (Sweden)

    Cupolillo Elisa

    1998-01-01

    Full Text Available Our results have shown the wide diversity of parasites within New World Leishmania. Biochemical and molecular characterization of species within the genus has revealed that much of the population heterogeneity has a genetic basis. The source of genetic diversity among Leishmania appears to arise from predominantly asexual, clonal reproduction, although occasional bouts of sexual reproduction can not be ruled out. Genetic variation is extensive with some clones widely distributed and others seemingly unique and localized to a particular endemic focus. Epidemiological studies of leishmaniasis has been directed to the ecology and dynamics of transmission of Leishmania species/variants, particularly in localized areas. Future research using molecular techniques should aim to identify and follow Leishmania types in nature and correlate genetic typing with important clinical characteristics such as virulence, pathogenicity, drug resistance and antigenic variation. The epidemiological significance of such variation not only has important implications for the control of the leishmaniases, but would also help to elucidate the evolutionary biology of the causative agents.

  14. CRISPR associated diversity within a population of Sulfolobus islandicus.

    Directory of Open Access Journals (Sweden)

    Nicole L Held

    2010-09-01

    Full Text Available Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations.We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population.The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population.

  15. Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

    Directory of Open Access Journals (Sweden)

    Alicia R Martin

    2014-08-01

    Full Text Available Large-scale sequencing efforts have documented extensive genetic variation within the human genome. However, our understanding of the origins, global distribution, and functional consequences of this variation is far from complete. While regulatory variation influencing gene expression has been studied within a handful of populations, the breadth of transcriptome differences across diverse human populations has not been systematically analyzed. To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of EBV transformed lymphoblastoid cell lines derived from 45 individuals in the Human Genome Diversity Panel (HGDP. The populations sampled span the geographic breadth of human migration history and include Namibian San, Mbuti Pygmies of the Democratic Republic of Congo, Algerian Mozabites, Pathan of Pakistan, Cambodians of East Asia, Yakut of Siberia, and Mayans of Mexico. We discover that approximately 25.0% of the variation in gene expression found amongst individuals can be attributed to population differences. However, we find few genes that are systematically differentially expressed among populations. Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations. Allelic expression analyses indicate that previously mapped common regulatory variants identified in eight populations from the International Haplotype Map Phase 3 project have similar effects in our seven sampled HGDP populations, suggesting that the cellular effects of common variants are shared across diverse populations. Together, these results provide a resource for studies analyzing functional differences across populations by estimating the degree of shared gene expression, alternative splicing, and

  16. Genetic Diversity and Structure of the Apiosporina morbosa Populations on Prunus spp.

    Science.gov (United States)

    Zhang, Jinxiu; Fernando, W G Dilantha; Remphrey, William R

    2005-08-01

    ABSTRACT Populations of Apiosporina morbosa collected from 15 geographic locations in Canada and the United States and three host species, Prunus virginiana, P. pensylvanica, and P. padus, were evaluated using the sequence-related amplified polymorphism (SRAP) technique to determine their genetic diversity and population differentiation. Extensive diversity was detected in the A. morbosa populations, including 134 isolates from Canada and the United States, regardless of the origin of the population. The number of polymorphic loci varied from 6.9 to 82.8% in the geographic populations, and from 41.4 to 79.3% in the populations from four host genotypes based on 58 polymorphic fragments. In all, 44 to 100% of isolates in the geographic populations and 43.6 to 76.2% in populations from four host genotypes represented unique genotypes. Values of heterozygosity (H) varied from 2.8 to 28.3% in the geographic populations and 10.2 to 26.1% in the populations from four host genotypes. In general, the A. morbosa populations sampled from wild chokecherry showed a higher genetic diversity than those populations collected from other host species, whereas the populations isolated from cultivated chokecherry, P. virginiana 'Shubert Select', showed a reduction of genetic diversity compared with populations from wild P. virginiana. Significant population differentiation was found among both the geographic populations (P virginiana were closely clustered, and no population differentiation was detected except for the populations from Morris, Morden, and Winnipeg, Manitoba, Canada. Furthermore, the populations from P. virginiana in the same geographic locations had higher genetic identity and closer genetic distance to each other compared with those from different locations. Four populations from P. virginiana, P. pensylvanica, and P. padus, were significantly differentiated from each other (P P> = 0.334). Indirect estimation of gene flow showed that significant restricted gene flow

  17. Genetic diversity and differentiation of Mongolian indigenous cattle populations

    Energy Technology Data Exchange (ETDEWEB)

    Lkhagva, B [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya) and Mongolian State Agricultural University, Zaisan, Ulaanbaatar 210153 (Mongolia); Ochieng, J W; Hanotte, O; Jianlin, H [International Livestock Research Institute - ILRI, P.O. Box 30709, Nairobi (Kenya); Yoon, D H [National Livestock Research Institute, RDA, 441-350, Suwon (Korea)

    2003-07-01

    Livestock production plays an important role in Mongolian economy. Over the last decade it has contributed to around 80-90% of the gross domestic agricultural products and to 30% of the revenues generated from exportations. Cattle is one of the five traditional and most important livestock species of Mongolia together with horse, sheep, goat and camel. Out of a total of 1.57 millions Mongolian cattle, 1.55 millions supposedly belong to three indigenous Bos taurus cattle breeds, namely Mongol, Selenge and Khalkhun Golun, all herded under extensive pastoral systems. Indigenous Mongolian cattle are generally small but look sturdy and strong. They have a well-off coat of hair, solid forward looking shoulders and short stubby snouts, and they are used for meat, milk and transport. Beef production contributes to 30% of the total meat supply in Mongolia. The Mongol breed is by the far the commonest with 1.53 million animals and it is found almost throughout the country. The Selenge breed, found in Selenge province and numbering 9000 heads, was developed in middle of the 20th century by crossing the Kazakh Whiteheaded with the local Mongol cattle. The Khalkhun Golun breed was developed from local Mongol cattle and it is distributed in Eastern and Suhbaatar provinces with about 10,000 heads. Until now, to the best of our knowledge, only a single population of Mongolian cattle has been studied with microsatellite DNA markers and no information is available on the genetic relationship between the Mongolian indigenous cattle breeds. In this study, we collected samples from two populations of the Mongol cattle (sampled at Ikhtamir soum in North Hangay province and Tsogt soum in Govi Altay province) and one population of the Khalkhun Golun cattle (sampled at Tumentsogt soum in Suhbaatar province). Samples were characterised with nine microsatellite markers MGTG4B, ILSTS005, ILSTS006, ILSTS008, ILSTS023, ILSTS028, ILSTS036, ILSTS050 and ILSTS103. To assess the genetic diversity

  18. De novo assembly of highly diverse viral populations

    Directory of Open Access Journals (Sweden)

    Yang Xiao

    2012-09-01

    Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  19. Genetic diversity in wild populations of Paulownia fortune.

    Science.gov (United States)

    Li, H Y; Ru, G X; Zhang, J; Lu, Y Y

    2014-11-01

    The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138-1.2726), Nei's genetic diversity (0.1566-0.1887), and Shannon's information index (0.2692-0.3117) indicated a plentiful genetic diversity and different among Paulownia fortunei populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.

  20. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  1. Plasmodium vivax Diversity and Population Structure across Four Continents.

    Science.gov (United States)

    Koepfli, Cristian; Rodrigues, Priscila T; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y M; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8), intermediate in the South Pacific (8.1-9.9) Madagascar and Sudan (7.9-8.4), and lowest in South America and Central Asia (5.5-7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11-0.16) between South American and all other populations, and lowest (0.04-0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

  2. Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution

    Science.gov (United States)

    2012-01-01

    Background The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. Results The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. Conclusions

  3. Interactive diversity promotes the evolution of cooperation in structured populations

    International Nuclear Information System (INIS)

    Su, Qi; Li, Aming; Zhou, Lei; Wang, Long

    2016-01-01

    Evolutionary games on networks traditionally assume that each individual adopts an identical strategy to interact with all its neighbors in each generation. Considering the prevalent diversity of individual interactions in the real society, here we propose the concept of interactive diversity, which allows individuals to adopt different strategies against different neighbors in each generation. We investigate the evolution of cooperation based on the edge dynamics rather than the traditional nodal dynamics in networked systems. The results show that, without invoking any other mechanisms, interactive diversity drives the frequency of cooperation to a high level for a wide range of parameters in both well-mixed and structured populations. Even in highly connected populations, cooperation still thrives. When interactive diversity and large topological heterogeneity are combined together, however, in the relaxed social dilemma, cooperation level is lower than that with just one of them, implying that the combination of many promotive factors may make a worse outcome. By an analytical approximation, we get the condition under which interactive diversity provides more advantages for cooperation than traditional evolutionary dynamics does. Numerical simulations validating the approximation are also presented. Our work provides a new line to explore the latent relation between the ubiquitous cooperation and individuals’ distinct responses in different interactions. The presented results suggest that interactive diversity should receive more attention in pursuing mechanisms fostering cooperation. (paper)

  4. Genetic diversity of Annona senegalensis Pers. populations as ...

    African Journals Online (AJOL)

    Annona senegalensis Pers. is one of the wild fruit tree for domestication in southern Africa. An assessment of the genetic diversity in A. senegalensis would assist in planning for future germplasm collection, conservation and fruit domestication programmes. During 2004 to 2006 nine populations were collected from different ...

  5. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

  6. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    ONOS

    2010-01-25

    Jan 25, 2010 ... Population dynamics of soil microbes and diversity of ... 25.78, 25.78, 86.26, 24.73, 68.0, 26.8 and 26.8 kDa proteins and equivalent to Cyt, Cry5 and Cry2 toxins ..... Molecular weight (kDa) of protein fractions of the BT isolates.

  7. Speaking of Health: Assessing Health Communication Strategies for Diverse Populations

    National Research Council Canada - National Science Library

    2002-01-01

    ... for their special competences and with regard for appropriate balance. Support for this project was provided by the Institute of Medicine. The views presented in this report are those of the Institute of Medicine Committee on Communication for Behavior Change in the 21st Century: Improving the Health of Diverse Populations and are not necessarily those of ...

  8. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  9. Genetic diversity in Kenyan populations of Acacia senegal (L.) willd ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... species grows to 2-15 m tall with a flat or rounded crown. (Maundu et al., 1999). ... Our knowledge on the structure of genetic diversity of. A. senegal in Kenya ..... conclusion that spatial organization of local populations and the ...

  10. Low genetic diversity of Phytophthora infestans population in potato ...

    African Journals Online (AJOL)

    AJL

    genetic diversity of P. infestans and geographical origin. These results provided a foundation for making integrated control measures in the future. Key words: Phytophthora infestans, population genetics, simple-sequence repeat (SSR), potato late blight. INTRODUCTION. Phytophthora infestans (Mont.) de Bary, causing the ...

  11. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust

    Directory of Open Access Journals (Sweden)

    Ulisses eNunes da Rocha

    2015-04-01

    Full Text Available Biological Soil Crusts (BSCs are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light and isolation strategies (media with varying nutrient availability and protection from oxidative stress we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology, 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.

  12. Population genetic diversity and hybrid detection in captive zebras.

    Science.gov (United States)

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-08-21

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra.

  13. Population diversity in Pacific herring of the Puget Sound, USA.

    Science.gov (United States)

    Siple, Margaret C; Francis, Tessa B

    2016-01-01

    Demographic, functional, or habitat diversity can confer stability on populations via portfolio effects (PEs) that integrate across multiple ecological responses and buffer against environmental impacts. The prevalence of these PEs in aquatic organisms is as yet unknown, and can be difficult to quantify; however, understanding mechanisms that stabilize populations in the face of environmental change is a key concern in ecology. Here, we examine PEs in Pacific herring (Clupea pallasii) in Puget Sound (USA) using a 40-year time series of biomass data for 19 distinct spawning population units collected using two survey types. Multivariate auto-regressive state-space models show independent dynamics among spawning subpopulations, suggesting that variation in herring production is partially driven by local effects at spawning grounds or during the earliest life history stages. This independence at the subpopulation level confers a stabilizing effect on the overall Puget Sound spawning stock, with herring being as much as three times more stable in the face of environmental perturbation than a single population unit of the same size. Herring populations within Puget Sound are highly asynchronous but share a common negative growth rate and may be influenced by the Pacific Decadal Oscillation. The biocomplexity in the herring stock shown here demonstrates that preserving spatial and demographic diversity can increase the stability of this herring population and its availability as a resource for consumers.

  14. Lowered Diversity and Increased Inbreeding Depression within Peripheral Populations of Wild Rice Oryza rufipogon.

    Science.gov (United States)

    Gao, Li-Zhi; Gao, Cheng-Wen

    2016-01-01

    The distribution of genetic variability from the interior towards the periphery of a species' range is of great interest to evolutionary biologists. Although it has been long presumed that population genetic variation should decrease as a species' range is approached, results of empirical investigations still remain ambiguous. Knowledge regarding patterns of genetic variability as well as affected factors is particularly not conclusive in plants. To determine genetic divergence in peripheral populations of the wild rice Oryza rufipogon Griff. from China, genetic diversity and population structure were studied in five northern & northeastern peripheral and 16 central populations using six microsatellite loci. We found that populations resided at peripheries of the species possessed markedly decreased microsatellite diversity than those located in its center. Population size was observed to be positively correlated with microsatellite diversity. Moreover, there are significantly positive correlations between levels of microsatellite diversity and distances from the northern and northeastern periphery of this species. To investigate genetic structure and heterozygosity variation between generations of O. rufipogon, a total of 2382 progeny seeds from 186 maternal families were further assayed from three peripheral and central populations, respectively. Peripheral populations exhibited significantly lower levels of heterozygosities than central populations for both seed and maternal generations. In comparisons with maternal samples, significantly low observed heterozygosity (HO) and high heterozygote deficit within populations (FIS) values were detected in seed samples from both peripheral and central populations. Significantly lower observed heterozygosity (HO) and higher FIS values were further observed in peripheral populations than those in central populations for seed samples. The results indicate an excess of homozygotes and thus high inbreeding depression in

  15. Do wild chimpanzee populations develop diverse cultures? [Latest Thinking

    OpenAIRE

    Boesch, C.

    2017-01-01

    Humans pride themselves on having extensive and diverse cultures. However, cultures can also be observed in animals. The research presented in this video aims at understanding the cultures of wild chimpanzee populations in several African countries and how they differ from each other. As chimpanzees avoid human contact, CHRISTOPHE BOESCH explains, the research team conducted the study by setting up camera traps to catch chimpanzee behavior on video. Forty locations were carefully selected to ...

  16. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations. © 2012 Blackwell Verlag GmbH.

  17. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data

    Science.gov (United States)

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-01-01

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

  18. Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

    Science.gov (United States)

    Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

    2017-09-01

    The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population

  19. Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

    Science.gov (United States)

    Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P

    1999-12-01

    Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.

  20. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina.

    Science.gov (United States)

    Anello, M; Daverio, M S; Romero, S R; Rigalt, F; Silbestro, M B; Vidal-Rioja, L; Di Rocco, F

    2016-02-01

    The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.

  1. The significance of nonviable eggs for Daphnia population dynamics

    NARCIS (Netherlands)

    Boersma, M.; Vijverberg, J.

    1995-01-01

    Egg mortality was studied in populations of Daphnia galeata, Daphnia cucullata, and the hybrid between these species. In Tjeukemeer, a shallow eutrophic lake in the Netherlands, egg mortality in daphnids manifested itself as an apparent increase in the frequency of eggs in the early developmental

  2. Genetic diversity of six populations of red hybrid tilapia, using microsatellites genetic markers

    Directory of Open Access Journals (Sweden)

    Boris Briñez R.

    2011-05-01

    Full Text Available Objective. To determine and evaluate the genetic diversity of six populations of red hybrid tilapia, with the purpose to assess the potential benefit of a future breeding program conducted at the Research Center for Aquaculture (Ceniacua, Colombia. Material and methods. A total of 300 individuals, representing a wide genetic variability, were genotyped using a fluorescent microsatellite marker set of 5 gene-based SSRs in 6 different farms belonging to 4 States of Colombia. Results. The result showed that the mean number of alleles per locus per population was 8.367. The population 5 had the highest mean number of alleles with 9.6 alleles, followed by population 4 with 9.4 alleles, population 2 with 9.2, population 3 with 8.0, population 1 with 7.2 and population 6 with 6.8 alleles. The analysis of the distribution of genetic variation was (17.32% among population, while among individuals within populations was (28.55% and within individuals was high (54.12%. The standard diversity indices showed that population 4 was the more variable (mean He=0.837 followed by population 1 (mean He=0.728, population 3 (mean He=0.721, population 5 (mean He=0.705, population 2 (mean He=0.690, population 6 (mean He=0.586. Highly significant deviations from Hardy–Weinberg, exhibited all of the populations, mostly due to deficits of heterozygotes. Genotype frequencies at loci UNH 106 of population 5 and loci UNH 172 of population 6 were Hardy-Weinberg equilibrium (HWE. Conclusions. The results of this study, contribute to the genetic breeding program of Tilapia, conduced by the Research Center for Aquaculture. The Fst distance showed that the samples are differentiated genetically and it is possible to use at the beginning of the genetic program. However, it is recommended to introduce others individuals to the crossbreeding program.

  3. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  4. Significant population genetic structure detected in the rock bream Oplegnathus fasciatus (Temminck & Schlegel, 1844) inferred from fluorescent-AFLP analysis

    Science.gov (United States)

    Xiao, Yongshuang; Ma, Daoyuan; Xu, Shihong; Liu, Qinghua; Wang, Yanfeng; Xiao, Zhizhong; Li, Jun

    2016-05-01

    Oplegnathus fasciatus (rock bream) is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplified fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei's genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance (AMOVA) showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index F st ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O. fasciatus populations examined should comprise two stocks.

  5. Invasion success in Cogongrass (Imperata cylindrica): A population genetic approach exploring genetic diversity and historical introductions

    Science.gov (United States)

    Rima D. Lucardi; Lisa E. Wallace; Gary N. Ervin

    2014-01-01

    Propagule pressure significantly contributes to and limits the potential success of a biological invasion, especially during transport, introduction, and establishment. Events such as multiple introductions of foreign parent material and gene flow among them can increase genetic diversity in founding populations, often leading to greater invasion success. We applied...

  6. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  7. Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus).

    Science.gov (United States)

    Chaves, Paulo B; Alvarenga, Clara S; Possamai, Carla de B; Dias, Luiz G; Boubli, Jean P; Strier, Karen B; Mendes, Sérgio L; Fagundes, Valéria

    2011-01-01

    Social, ecological, and historical processes affect the genetic structure of primate populations, and therefore have key implications for the conservation of endangered species. The northern muriqui (Brachyteles hypoxanthus) is a critically endangered New World monkey and a flagship species for the conservation of the Atlantic Forest hotspot. Yet, like other neotropical primates, little is known about its population history and the genetic structure of remnant populations. We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion. Bayesian and classic analyses show that this finding may be attributed to the joint contribution of female-biased dispersal, demographic stability, and a relatively large historic population size. Past population stability is consistent with a central Atlantic Forest Pleistocene refuge. In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST) = 0.49, Φ(CT) = 0.24), and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene. Genetic diversity is higher in populations living in larger areas (>2,000 hectares), but it is remarkably low in the species overall (θ = 0.018). Three populations occurring in protected reserves and one fragmented population inhabiting private lands harbor 22 out of 23 haplotypes, most of which are population-exclusive, and therefore represent patchy repositories of the species' genetic diversity. We suggest that these populations be treated as discrete units for conservation management purposes.

  8. Genetic diversity and population history of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus.

    Directory of Open Access Journals (Sweden)

    Paulo B Chaves

    Full Text Available Social, ecological, and historical processes affect the genetic structure of primate populations, and therefore have key implications for the conservation of endangered species. The northern muriqui (Brachyteles hypoxanthus is a critically endangered New World monkey and a flagship species for the conservation of the Atlantic Forest hotspot. Yet, like other neotropical primates, little is known about its population history and the genetic structure of remnant populations. We analyzed the mitochondrial DNA control region of 152 northern muriquis, or 17.6% of the 864 northern muriquis from 8 of the 12 known extant populations and found no evidence of phylogeographic partitions or past population shrinkage/expansion. Bayesian and classic analyses show that this finding may be attributed to the joint contribution of female-biased dispersal, demographic stability, and a relatively large historic population size. Past population stability is consistent with a central Atlantic Forest Pleistocene refuge. In addition, the best scenario supported by an Approximate Bayesian Computation analysis, significant fixation indices (Φ(ST = 0.49, Φ(CT = 0.24, and population-specific haplotypes, coupled with the extirpation of intermediate populations, are indicative of a recent geographic structuring of genetic diversity during the Holocene. Genetic diversity is higher in populations living in larger areas (>2,000 hectares, but it is remarkably low in the species overall (θ = 0.018. Three populations occurring in protected reserves and one fragmented population inhabiting private lands harbor 22 out of 23 haplotypes, most of which are population-exclusive, and therefore represent patchy repositories of the species' genetic diversity. We suggest that these populations be treated as discrete units for conservation management purposes.

  9. MHC class II diversity of koala (Phascolarctos cinereus) populations across their range.

    Science.gov (United States)

    Lau, Q; Jaratlerdsiri, W; Griffith, J E; Gongora, J; Higgins, D P

    2014-10-01

    Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.

  10. Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

    Science.gov (United States)

    Chapman, Duane C.; Chen, Qin; Wang, Chenghui; Zhao, Jinlian; Lu, Guoqing; Zsigmond, Jeney; Li, Si-Fa

    2012-01-01

    Grass carp (Ctenopharyngodon idella), a freshwater species native to China, has been introduced to about 100 countries/regions and poses both biological and environmental challenges to the receiving ecosystems. In this study, we analyzed genetic variation in grass carp from three introduced river systems (Mississippi River Basin in US, Danube River in Hungary, and Tone River in Japan) as well as its native ranges (Yangtze, Pearl, and Amur Rivers) in China using 21 novel microsatellite loci. The allelic richness, observed heterozygosity, and within-population gene diversity were found to be lower in the introduced populations than in the native populations, presumably due to the small founder population size of the former. Significant genetic differentiation was found between all pairwise populations from different rivers. Both principal component analysis and Bayesian clustering analysis revealed obvious genetic distinction between the native and introduced populations. Interestingly, genetic bottlenecks were detected in the Hungarian and Japanese grass carp populations, but not in the North American population, suggesting that the Mississippi River Basin grass carp has experienced rapid population expansion with potential genetic diversification during the half-century since its introduction. Consequently, the combined forces of the founder effect, introduction history, and rapid population expansion help explaining the observed patterns of genetic diversity within and among both native and introduced populations of the grass carp.

  11. Genetic diversity and natural selection footprints of the glycine amidinotransferase gene in various human populations.

    Science.gov (United States)

    Khan, Asifullah; Tian, Lei; Zhang, Chao; Yuan, Kai; Xu, Shuhua

    2016-01-05

    The glycine amidinotransferase gene (GATM) plays a vital role in energy metabolism in muscle tissues and is associated with multiple clinically important phenotypes. However, the genetic diversity of the GATM gene remains poorly understood within and between human populations. Here we analyzed the 1,000 Genomes Project data through population genetics approaches and observed significant genetic diversity across the GATM gene among various continental human populations. We observed considerable variations in GATM allele frequencies and haplotype composition among different populations. Substantial genetic differences were observed between East Asian and European populations (FST = 0.56). In addition, the frequency of a distinct major GATM haplotype in these groups was congruent with population-wide diversity at this locus. Furthermore, we identified GATM as the top differentiated gene compared to the other statin drug response-associated genes. Composite multiple analyses identified signatures of positive selection at the GATM locus, which was estimated to have occurred around 850 generations ago in European populations. As GATM catalyzes the key step of creatine biosynthesis involved in energy metabolism, we speculate that the European prehistorical demographic transition from hunter-gatherer to farming cultures was the driving force of selection that fulfilled creatine-based metabolic requirement of the populations.

  12. Analysis of Population Diversity of Dynamic Probabilistic Particle Swarm Optimization Algorithms

    Directory of Open Access Journals (Sweden)

    Qingjian Ni

    2014-01-01

    Full Text Available In evolutionary algorithm, population diversity is an important factor for solving performance. In this paper, combined with some population diversity analysis methods in other evolutionary algorithms, three indicators are introduced to be measures of population diversity in PSO algorithms, which are standard deviation of population fitness values, population entropy, and Manhattan norm of standard deviation in population positions. The three measures are used to analyze the population diversity in a relatively new PSO variant—Dynamic Probabilistic Particle Swarm Optimization (DPPSO. The results show that the three measure methods can fully reflect the evolution of population diversity in DPPSO algorithms from different angles, and we also discuss the impact of population diversity on the DPPSO variants. The relevant conclusions of the population diversity on DPPSO can be used to analyze, design, and improve the DPPSO algorithms, thus improving optimization performance, which could also be beneficial to understand the working mechanism of DPPSO theoretically.

  13. PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations.

    Science.gov (United States)

    Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi; Xu, Shuhua

    2018-01-04

    There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

    DEFF Research Database (Denmark)

    Schou, Mads F.; Loeschcke, Volker; Bechsgaard, Jesper

    2017-01-01

    fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent...

  15. Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations.

    Science.gov (United States)

    Saville, Amanda; Charles, Melodi; Chavan, Suchitra; Muñoz, Miguel; Gómez-Alpizar, Luis; Ristaino, Jean Beagle

    2017-12-01

    Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

  16. Membrane bioreactor wastewater treatment plants reveal diverse yeast and protist communities of potential significance in biofouling.

    Science.gov (United States)

    Liébana, Raquel; Arregui, Lucía; Belda, Ignacio; Gamella, Luis; Santos, Antonio; Marquina, Domingo; Serrano, Susana

    2015-01-01

    The yeast community was studied in a municipal full-scale membrane bioreactor wastewater treatment plant (MBR-WWTP). The unexpectedly high diversity of yeasts indicated that the activated sludge formed a suitable environment for them to proliferate, with cellular concentrations of 2.2 ± 0.8 × 10(3) CFU ml(-1). Sixteen species of seven genera were present in the biological reactor, with Ascomycetes being the most prevalent group (93%). Most isolates were able to grow in a synthetic wastewater medium, adhere to polyethylene surfaces, and develop biofilms of variable complexity. The relationship between yeast populations and the protists in the MBR-WWTP was also studied, revealing that some protist species preyed on and ingested yeasts. These results suggest that yeast populations may play a role in the food web of a WWTP and, to some extent, contribute to membrane biofouling in MBR systems.

  17. SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

    Science.gov (United States)

    Choudhary, Shashi Bhushan; Sharma, Hariom Kumar; Kumar, Arroju Anil; Maruthi, Rangappa Thimmaiah; Mitra, Jiban; Chowdhury, Isholeena; Singh, Binay Kumar; Karmakar, Pran Gobinda

    2017-02-01

    A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI=0.46; He=0.31; P=85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P=0.01. The maximum Nei's unbiased genetic distance (D=0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm. Copyright © 2016 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  18. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler.

    Science.gov (United States)

    Wright, David J; Spurgin, Lewis G; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

    2014-05-01

    Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool. © 2014 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  19. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers.

    Science.gov (United States)

    Filippi, Carla V; Aguirre, Natalia; Rivas, Juan G; Zubrzycki, Jeremias; Puebla, Andrea; Cordes, Diego; Moreno, Maria V; Fusari, Corina M; Alvarez, Daniel; Heinz, Ruth A; Hopp, Horacio E; Paniego, Norma B; Lia, Veronica V

    2015-02-13

    Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent

  20. Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa

    Directory of Open Access Journals (Sweden)

    Mobegi Victor A

    2012-07-01

    Full Text Available Abstract Background Malaria parasite population genetic structure varies among areas of differing endemicity, but this has not been systematically studied across Plasmodium falciparum populations in Africa where most infections occur. Methods Ten polymorphic P. falciparum microsatellite loci were genotyped in 268 infections from eight locations in four West African countries (Republic of Guinea, Guinea Bissau, The Gambia and Senegal, spanning a highly endemic forested region in the south to a low endemic Sahelian region in the north. Analysis was performed on proportions of mixed genotype infections, genotypic diversity among isolates, multilocus standardized index of association, and inter-population differentiation. Results Each location had similar levels of pairwise genotypic diversity among isolates, although there were many more mixed parasite genotype infections in the south. Apart from a few isolates that were virtually identical, the multilocus index of association was not significant in any population. Genetic differentiation between populations was low (most pairwise FST values  Conclusions Although proportions of mixed genotype infections varied with endemicity as expected, population genetic structure was similar across the diverse sites. Very substantial reduction in transmission would be needed to cause fragmented or epidemic sub-structure in this region.

  1. Population diversity of aeluropus lagopoides: a potential cash crop for saline land

    International Nuclear Information System (INIS)

    Ahmed, M.Z.; Gulzar, S.; Ahmed, M.Z.; Kikuchi, A.

    2011-01-01

    Aeluropus lagopoides is a salt tolerant grass which propagates both through genets and ramets. Six disjunct populations of A. lagopoides from Pakistan were selected to test the hypothesis that genetic diversity would be low within but higher among populations. Genetic diversity was investigated using RAPD markers. AMOVA showed higher genetic diversity within population (74%) and lower among population (26%). Furthermore, there were no genetic differences between coastal and inland populations. However, substantial (11%) genetic variation existed among populations of Sindh and Balochistan. Higher genetic diversity within populations are possibly due to physical disturbances that may provide more opportunity for establishment of seeds and increase the possibility of out crossing. Low diversity among populations or between coastal and inland populations indicates fragmentation of a single meta-population due to anthropogenic activity. Geographical barrier between Sindh and Balochistan, appears to mediate gene flow among populations of A. lagopoides. (author)

  2. Genetic health and population monitoring of two small black bear (Ursus americanus populations in Alabama, with a regional perspective of genetic diversity and exchange.

    Directory of Open Access Journals (Sweden)

    John P Draper

    Full Text Available One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I., the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33, and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I., relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65, and showed a high level of genetic connectivity with surrounding populations.

  3. Genetic health and population monitoring of two small black bear (Ursus americanus) populations in Alabama, with a regional perspective of genetic diversity and exchange.

    Science.gov (United States)

    Draper, John P; Waits, Lisette P; Adams, Jennifer R; Seals, Christopher L; Steury, Todd D

    2017-01-01

    One of the major concerns in conservation today is the loss of genetic diversity which is a frequent consequence of population isolation and small population sizes. Fragmentation of populations and persecution of carnivores has posed a substantial threat to the persistence of free ranging carnivores in North America since the arrival of European settlers. Black bears have seen significant reductions in range size from their historic extent, which is most pronounced in the southeastern United States and even more starkly in Alabama where until recently bears were reduced to a single geographically isolated population in the Mobile River Basin. Recently a second population has naturally re-established itself in northeastern Alabama. We sought to determine size, genetic diversity and genetic connectivity for these two populations in relation to other regional populations. Both populations of black bears in Alabama had small population sizes and had moderate to low genetic diversity, but showed different levels of connectivity to surrounding populations of bears. The Mobile River Basin population had a small population size at only 86 individuals (76-124, 95% C.I.), the lowest genetic diversity of compared populations (richness = 2.33, Ho and He = 0.33), and showed near complete genetic isolation from surrounding populations across multiple tests. The newly recolonizing population in northeastern Alabama had a small but growing population doubling in 3 years (34 individuals 26-43, 95% C.I.), relatively moderate genetic diversity compared to surrounding populations (richness = 3.32, Ho = 0.53, He = 0.65), and showed a high level of genetic connectivity with surrounding populations.

  4. Demographic collapse and low genetic diversity of the Irrawaddy dolphin population inhabiting the Mekong River.

    Science.gov (United States)

    Krützen, Michael; Beasley, Isabel; Ackermann, Corinne Y; Lieckfeldt, Dietmar; Ludwig, Arne; Ryan, Gerard E; Bejder, Lars; Parra, Guido J; Wolfensberger, Rebekka; Spencer, Peter B S

    2018-01-01

    In threatened wildlife populations, it is important to determine whether observed low genetic diversity may be due to recent anthropogenic pressure or the consequence of historic events. Historical size of the Irrawaddy dolphin (Orcaella brevirostris) population inhabiting the Mekong River is unknown and there is significant concern for long-term survival of the remaining population as a result of low abundance, slow reproduction rate, high neonatal mortality, and continuing anthropogenic threats. We investigated population structure and reconstructed the demographic history based on 60 Irrawaddy dolphins samples collected between 2001 and 2009. The phylogenetic analysis indicated reciprocal monophyly of Mekong River Orcaella haplotypes with respect to haplotypes from other populations, suggesting long-standing isolation of the Mekong dolphin population from other Orcaella populations. We found that at least 85% of all individuals in the two main study areas: Kratie and Stung Treng, bore the same mitochondrial haplotype. Out of the 21 microsatellite loci tested, only ten were polymorphic and exhibited very low levels of genetic diversity. Both individual and frequency-based approaches suggest very low and non-significant genetic differentiation of the Mekong dolphin population. Evidence for recent bottlenecks was equivocal. Some results suggested a recent exponential decline in the Mekong dolphin population, with the current size being only 5.2% of the ancestral population. In order for the Mekong dolphin population to have any potential for long-term survival, it is imperative that management priorities focus on preventing any further population fragmentation or genetic loss, reducing or eliminating anthropogenic threats, and promoting connectivity between all subpopulations.

  5. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  6. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Science.gov (United States)

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  7. Low genetic diversity and minimal population substructure in the endangered Florida manatee: implications for conservation

    Science.gov (United States)

    Tucker, Kimberly Pause; Hunter, Margaret E.; Bonde, Robert K.; Austin, James D.; Clark, Ann Marie; Beck, Cathy A.; McGuire, Peter M.; Oli, Madan K.

    2012-01-01

    Species of management concern that have been affected by human activities typically are characterized by low genetic diversity, which can adversely affect their ability to adapt to environmental changes. We used 18 microsatellite markers to genotype 362 Florida manatees (Trichechus manatus latirostris), and investigated genetic diversity, population structure, and estimated genetically effective population size (Ne). The observed and expected heterozygosity and average number of alleles were 0.455 ± 0.04, 0.479 ± 0.04, and 4.77 ± 0.51, respectively. All measures of Florida manatee genetic diversity were less than averages reported for placental mammals, including fragmented or nonideal populations. Overall estimates of differentiation were low, though significantly greater than zero, and analysis of molecular variance revealed that over 95% of the total variance was among individuals within predefined management units or among individuals along the coastal subpopulations, with only minor portions of variance explained by between group variance. Although genetic issues, as inferred by neutral genetic markers, appear not to be critical at present, the Florida manatee continues to face demographic challenges due to anthropogenic activities and stochastic factors such as red tides, oil spills, and disease outbreaks; these can further reduce genetic diversity of the manatee population.

  8. Low genetic diversity in Antarctic populations of the lichen-forming ascomycete Cetraria aculeata and its photobiont

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    Stephanie Domaschke

    2012-03-01

    Full Text Available Lichens, symbiotic associations of fungi (mycobionts and green algae or cyanobacteria (photobionts, are poikilohydric organisms that are particularly well adapted to withstand adverse environmental conditions. Terrestrial ecosystems of the Antarctic are therefore largely dominated by lichens. The effects of global climate change are especially pronounced in the maritime Antarctic and it may be assumed that the lichen vegetation will profoundly change in the future. The genetic diversity of populations is closely correlated to their ability to adapt to changing environmental conditions and to their future evolutionary potential. In this study, we present evidence for low genetic diversity in Antarctic mycobiont and photobiont populations of the widespread lichen Cetraria aculeata. We compared between 110 and 219 DNA sequences from each of three gene loci for each symbiont. A total of 222 individuals from three Antarctic and nine antiboreal, temperate and Arctic populations were investigated. The mycobiont diversity is highest in Arctic populations, while the photobionts are most diverse in temperate regions. Photobiont diversity decreases significantly towards the Antarctic but less markedly towards the Arctic, indicating that ecological factors play a minor role in determining the diversity of Antarctic photobiont populations. Richness estimators calculated for the four geographical regions suggest that the low genetic diversity of Antarctic populations is not a sampling artefact. Cetraria aculeata appears to have diversified in the Arctic and subsequently expanded its range into the Southern Hemisphere. The reduced genetic diversity in the Antarctic is most likely due to founder effects during long-distance colonization.

  9. Genetic diversity in Oryza glumaepatula wild rice populations in Costa Rica and possible gene flow from O. sativa.

    Science.gov (United States)

    Fuchs, Eric J; Meneses Martínez, Allan; Calvo, Amanda; Muñoz, Melania; Arrieta-Espinoza, Griselda

    2016-01-01

    Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation. Specimens from all known O. glumaepatula populations in Costa Rica were analyzed with 444 AFLP markers to characterize genetic diversity and structure. We also compared genetic diversity estimates between O. glumaepatula specimens and O. sativa commercial rice. Our results showed that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. Despite the restricted distribution of this species in Costa Rica, populations are fairly large, reducing the effects of drift on genetic diversity. We found a dismissible but significant structure (θ = 0.02 ± 0.001) among populations. A Bayesian structure analysis suggested that some individuals share a significant proportion of their genomes with O. sativa. These results suggest that gene flow from cultivated O. sativa populations may have occurred in the recent past. These results expose an important biohazard: recurrent hybridization may reduce the genetic diversity of this wild rice species. Introgression may transfer commercial traits into O. glumaepatula, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

  10. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

    insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

  11. In the time of significant generational diversity - surgical leadership must step up!

    Science.gov (United States)

    Money, Samuel R; O'Donnell, Mark E; Gray, Richard J

    2014-02-01

    The diverse attitudes and motivations of surgeons and surgical trainees within different age groups present an important challenge for surgical leaders and educators. These challenges to surgical leadership are not unique, and other industries have likewise needed to grapple with how best to manage these various age groups. The authors will herein explore management and leadership for surgeons in a time of age diversity, define generational variations within "Baby-Boomer", "Generation X" and "Generation Y" populations, and identify work ethos concepts amongst these three groups. The surgical community must understand and embrace these concepts in order to continue to attract a stellar pool of applicants from medical school. By not accepting the changing attitudes and motivations of young trainees and medical students, we may disenfranchise a high percentage of potential future surgeons. Surgical training programs will fill, but will they contain the highest quality trainees? Copyright © 2013 Royal College of Surgeons of Edinburgh (Scottish charity number SC005317) and Royal College of Surgeons in Ireland. Published by Elsevier Ltd. All rights reserved.

  12. Explaining the Linguistic Diversity of Sahul Using Population Models

    Science.gov (United States)

    Reesink, Ger; Singer, Ruth; Dunn, Michael

    2009-01-01

    The region of the ancient Sahul continent (present day Australia and New Guinea, and surrounding islands) is home to extreme linguistic diversity. Even apart from the huge Austronesian language family, which spread into the area after the breakup of the Sahul continent in the Holocene, there are hundreds of languages from many apparently unrelated families. On each of the subcontinents, the generally accepted classification recognizes one large, widespread family and a number of unrelatable smaller families. If these language families are related to each other, it is at a depth which is inaccessible to standard linguistic methods. We have inferred the history of structural characteristics of these languages under an admixture model, using a Bayesian algorithm originally developed to discover populations on the basis of recombining genetic markers. This analysis identifies 10 ancestral language populations, some of which can be identified with clearly defined phylogenetic groups. The results also show traces of early dispersals, including hints at ancient connections between Australian languages and some Papuan groups (long hypothesized, never before demonstrated). Systematic language contact effects between members of big phylogenetic groups are also detected, which can in some cases be identified with a diffusional or substrate signal. Most interestingly, however, there remains striking evidence of a phylogenetic signal, with many languages showing negligible amounts of admixture. PMID:19918360

  13. Radiation protection training for diverse general employee populations

    International Nuclear Information System (INIS)

    Copenhaver, E.D.; Houser, B.S.

    1986-01-01

    Radiation protection training for the general employee at the Oak Ridge National Laboratory has undergone a great deal of restructuring in the last two years. The number of personnel totally dedicated to nuclear facilities is less than a fifth of our employees and the percentage of contracted employees who are dedicated radiation workers is much smaller. However, the aging of our facilities and increasing emphasis on environmental control means that everyone needs to understand the basics of radiation protection. In accordance with changing DOE guidelines and internal ORNL policies, greater emphasis has been placed on keeping training focused on current issues, training the total workforce, and requiring some type of testing or feedback mechanism. This report describes efforts to instill respect, but not fear, of radiation in the work environment. Flexible tools are being developed to meet this objective for several diverse general employee populations. Continuing efforts include consideration of computer-based training for retraining, developing additional modules for specialized groups and jobs, and testing/documentation appropriate to each population segment. 6 refs

  14. Genetic diversity in populations of Maytenus dasyclada (Celastraceae in forest reserves and unprotected Araucaria forest remnants

    Directory of Open Access Journals (Sweden)

    Manuel Castilhos Reichmann

    Full Text Available ABSTRACT Understanding the genetic structure and diversity of plants is fundamental to their conservation and permits their sustainable use by local communities. The genus Maytenus (Celastraceae is composed of plants possessing pharmacological and antioxidant properties. However, the genetic and economic properties of the species M. dasyclada, a typical species of Araucaria forests in Brazil and Uruguay, have been little studied. In this work, the genetic structure and diversity of natural populations of M. dasyclada located in unprotected and preserved forest remnants were investigated using RAPD and isozymes markers. The results demonstrated that in areas of preservation, populations of M. dasyclada possess a relatively high degree of polymorphism and high values for Na, Ne, Shannon index, He and Ho, indicating high genetic variability. Moreover, these protected populations are very close to each other and potentially experience significant gene flow. The results presented here highlight the relevance of preservation areas for the conservation of M. dasyclada, and that populations inhabiting these areas could serve as a genetic source for the recovery of populations in regions where genetic diversity has been lost.

  15. Genetic diversity of six isolated populations of the leopard moth, Zeuzera pyrina (Lep: Zeuzeridae

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    Raheleh Dolati

    2017-03-01

    Full Text Available The leopard moth, Zeuzera pyrina (Lep: Zeuzeridae, is an important pest of a wide range of trees and shrubs including walnut and apple across the world. The natural populations of the leopard moth in different geographical areas of Iran show significant differences in some of their biological characteristics such as time of emergence, generation time and host specificity. So, we hypothesized that these populations may represent different subspecies that move toward a speciation event in their evolutionary route. In this study, we evaluated the genetic diversity of six different geographically isolated populations of the leopard moth using the sequence alignment of cytochrome oxidase c subunit one (COI. A fragment of 642 base pairs was amplified in all six populations and the phylogenetic tree was created based on sequenced fragments. Our results revealed significant differences in the nucleotide sequence of COI gene in these populations. Differences in climatic conditions of these regions seem to be the most powerful force driving this diversity among the studied populations.

  16. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations.

    Science.gov (United States)

    Tobler, M; Plath, M; Riesch, R; Schlupp, I; Grasse, A; Munimanda, G K; Setzer, C; Penn, D J; Moodley, Y

    2014-05-01

    The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

  17. Catastrophic floods may pave the way for increased genetic diversity in endemic artesian spring snail populations.

    Directory of Open Access Journals (Sweden)

    Jessica Worthington Wilmer

    Full Text Available The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as it requires both longitudinal genetic data sets and serendipitous timing. Our long-term study of the endemic aquatic invertebrates of the artesian spring ecosystem of arid central Australia has presented such an opportunity. Here we show a catastrophic flood event, which caused a near total population crash in an aquatic snail species (Fonscochlea accepta endemic to this ecosystem, may have led to enhanced levels of within species genetic diversity. Analyses of individuals sampled and genotyped from the same springs sampled both pre (1988-1990 and post (1995, 2002-2006 a devastating flood event in 1992, revealed significantly higher allelic richness, reduced temporal population structuring and greater effective population sizes in nearly all post flood populations. Our results suggest that the response of individual species to disturbance and severe population bottlenecks is likely to be highly idiosyncratic and may depend on both their ecology (whether they are resilient or resistant to disturbance and the stability of the environmental conditions (i.e. frequency and intensity of disturbances in which they have evolved.

  18. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

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    Flávio de Oliveira Francisco

    2013-01-01

    Full Text Available Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings.

  19. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

    Directory of Open Access Journals (Sweden)

    Brewer Marin

    2010-09-01

    Full Text Available Abstract Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated. Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern

  20. The Gut-Brain Axis in Healthy Females: Lack of Significant Association between Microbial Composition and Diversity with Psychiatric Measures.

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    Susan C Kleiman

    Full Text Available This study examined associations between the composition and diversity of the intestinal microbiota and measures of depression, anxiety, eating disorder psychopathology, stress, and personality in a group of healthy adult females.Female participants (n = 91 ages 19-50 years with BMI 18.5-25 kg/m2 were recruited from central North Carolina between July 2014 and March 2015. Participants provided a single fecal sample and completed an online psychiatric questionnaire that included five measures: (i Beck Anxiety Inventory; (ii Beck Depression Inventory-II; (iii Eating Disorder Examination-Questionnaire; (iv Perceived Stress Scale; and (v Mini International Personality Item Pool. Bacterial composition and diversity were characterized by Illumina sequencing of the 16S rRNA gene, and associations were examined using Kendall's tau-b correlation coefficient, in conjunction with Benjamini and Hochberg's False Discovery Rate procedure.We found no significant associations between microbial markers of gut composition and diversity and scores on psychiatric measures of anxiety, depression, eating-related thoughts and behaviors, stress, or personality in a large cohort of healthy adult females.This study was the first specifically to examine associations between the intestinal microbiota and psychiatric measures in healthy females, and based on 16S rRNA taxonomic abundances and diversity measures, our results do not suggest a strong role for the enteric microbe-gut-brain axis in normal variation on responses to psychiatric measures in this population. However, the role of the intestinal microbiota in the pathophysiology of psychiatric illness may be limited to more severe psychopathology.

  1. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

    Science.gov (United States)

    Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

    2009-07-14

    structure of P. falciparum populations in Thailand with those in the French Guyana, Congo and Cameroon revealed a significant genetic differentiation between all of them, except the two African countries, whilst the genetic variability of P. falciparum amongst countries showed overlapping distributions. Plasmodium falciparum shows genetically structured populations across local areas of Thailand. Although Thailand is considered to be a low transmission area, a relatively high level of genetic diversity and no linkage disequilibrium was found in five of the studied areas, the exception being the Yala province (Southern peninsular Thailand), where a clonal population structure was revealed and in Kanchanaburi province (Western Thailand). This finding is particularly relevant in the context of malaria control, because it could help in understanding the special dynamics of parasite populations in areas with different histories of, and exposure to, drug regimens.

  2. Genetic diversity and substantial population differentiation in Crassostrea hongkongensis revealed by mitochondrial DNA.

    Science.gov (United States)

    Li, Lu; Wu, Xiangyun; Yu, Ziniu

    2013-09-01

    The Hong Kong oyster, Crassostrea hongkongensis, is an important fisheries resource that is cultivated in the coastal waters of the South China Sea. Despite significant advances in understanding biological and taxonomic aspects of this species, no detailed study of its population genetic diversity in regions of extensive cultivation are available. Direct sequencing of the mtDNA cox1 gene region was used to investigate genetic variation within and between eleven C. hongkongensis populations collected from typical habitats. Sixty-two haplotypes were identified; only haplotype 2 (21.74% of total haplotypes) was shared among all the eleven populations, and most of the observed haplotypes were restricted to individual populations. Both AMOVA and FST analyses revealed significant population structure, and the isolation by distance (IBD) was confirmed. The highest local differentiation was observed between the sample pools from Guangxi versus Guangdong and Fujian, which are separated by a geographic barrier, the Leizhou Peninsula. Current knowledge from seed management suggests that seed transfer from Guangxi province has likely reduced the divergence that somewhat naturally exists between these pools. The findings from the present study could be useful for genetic management and may serve as a baseline by which to monitor future changes in genetic diversity, either due to natural or anthropogenic impacts. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Genetic diversity of Pinus halepensis Mill. populations detected by RAPD loci

    OpenAIRE

    Gómez , Aránzazu; Alía , Ricardo; Bueno , María

    2001-01-01

    International audience; Genetic diversity of Pinus halepensis Mill. was analysed in nine populations (six Spanish populations and one each from Tunisia, France and Greece). Twenty four RAPD loci were amplified with 60 megagametophyte DNA samples from each population. Populations' contribution to Nei gene diversity and to allelic richness were calculated. Results showed higher within population genetic variation but also a $G_{{\\rm ST}} = 13.6\\%$ higher than those detected in previous studies ...

  4. Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791: a bivalve with planktonic larval dispersion

    Directory of Open Access Journals (Sweden)

    Cinthya Cristina Bulhões Arruda

    2009-01-01

    Full Text Available Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe and both H5 and H9 (Prainha and Acupe. Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.

  5. Analysis of genetic diversity in Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers

    Directory of Open Access Journals (Sweden)

    Melka Melkaye G

    2012-03-01

    Full Text Available Abstract Background Studies of genetic diversity are essential in understanding the extent of differentiation between breeds, and in designing successful diversity conservation strategies. The objective of this study was to evaluate the level of genetic diversity within and between North American Brown Swiss (BS, n = 900, Jersey (JE, n = 2,922 and Holstein (HO, n = 3,535 cattle, using genotyped bulls. GENEPOP and FSTAT software were used to evaluate the level of genetic diversity within each breed and between each pair of the three breeds based on genome-wide SNP markers (n = 50,972. Results Hardy-Weinberg equilibrium (HWE exact test within breeds showed a significant deviation from equilibrium within each population (P st indicated that the combination of BS and HO in an ideally amalgamated population had higher genetic diversity than the other pairs of breeds. Conclusion Results suggest that the three bull populations have substantially different gene pools. BS and HO show the largest gene differentiation and jointly the highest total expected gene diversity compared to when JE is considered. If the loss of genetic diversity within breeds worsens in the future, the use of crossbreeding might be an option to recover genetic diversity, especially for the breeds with small population size.

  6. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality

    Science.gov (United States)

    Thomas, Geethu E.; Geetha, Kiran A.; Augustine, Lesly; Mamiyil, Sabu; Thomas, George

    2016-01-01

    Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically

  7. Does the parasite-mediated selection drive the MHC class IIB diversity in wild populations of European chub (Squalius cephalus)?

    Science.gov (United States)

    Seifertová, Mária; Jarkovský, Jiří; Šimková, Andrea

    2016-04-01

    The genes of major histocompatibility complex (MHC) provide an excellent opportunity to study host-parasite relationships because they are expected to evolve in response to parasites and variation in parasite communities. In this study, we investigated the potential role of parasite-mediated selection acting on MHC class IIB (DAB) genes in European chub (Squalius cephalus) natural populations. We found significant differences between populations in metazoan parasites, neutral and adaptive genetic diversities. The analyses based on pairwise data revealed that populations with dissimilar MHC allelic profiles were geographically distant populations with significantly different diversity in microsatellites and a dissimilar composition of parasite communities. The results from the generalized estimating equations method (GEE) on the level of individuals revealed that metazoan parasite load in European chub was influenced by the diversity of DAB alleles as well as by the diversity of neutral genetic markers and host traits reflecting condition and immunocompetence. The multivariate co-inertia analysis showed specific associations between DAB alleles and parasite species. DAB1-like alleles were more involved in associations with ectoparasites, while DAB3-like alleles were positively associated with endoparasites which could suggest potential differences between DAB genes caused by different selection pressure. Our study revealed that parasite-mediated selection is not the only variable affecting MHC diversity in European chub; however, we strongly support the role of neutral processes as the main driver of DAB diversity across populations. In addition, our study contributes to the understanding of the evolution of MHC genes in wild living fish.

  8. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

    Directory of Open Access Journals (Sweden)

    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  9. Ecological adaptation of diverse honey bee (Apis mellifera populations.

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    Robert Parker

    Full Text Available BACKGROUND: Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. RESULTS: Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. CONCLUSIONS: Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

  10. Ecological adaptation of diverse honey bee (Apis mellifera) populations.

    Science.gov (United States)

    Parker, Robert; Melathopoulos, Andony P; White, Rick; Pernal, Stephen F; Guarna, M Marta; Foster, Leonard J

    2010-06-15

    Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major 'omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

  11. Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation

    Science.gov (United States)

    Yao, Nasser; Martina, Kyalo; Dagne, Kifle; Wegary, Dagne; Tesfaye, Kassahun

    2017-01-01

    White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212

  12. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    Directory of Open Access Journals (Sweden)

    Najat El Moutchou

    2017-12-01

    Full Text Available The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05 from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population, resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  13. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    El Moutchou, N.; González-Martínez, A.M.; Chentouf, M.; Lairini, K.; Rodero, E.

    2017-07-01

    The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05) from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA) indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population), resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  14. Genetic diversity of the Northern Morocco goat population assessed with microsatellite markers

    International Nuclear Information System (INIS)

    El Moutchou, N.; González-Martínez, A.M.; Chentouf, M.; Lairini, K.; Rodero, E.

    2017-01-01

    The main goal of this work was to study the genetic diversity of the Northern Morocco goat population through the analysis of 19 microsatellites in 144 animals from 61 herds. To detect a possible population structure, three distinct geographic subpopulations were characterized as a function of climate and environmental influences. Most of the markers were highly polymorphic, and the results revealed considerable genetic variation across the studied loci. A total of 204 alleles were detected, with an average number of 10.7 per locus. The PIC average was 0.728, and four microsatellites showed a significant deviation (p< 0.05) from Hardy-Weinberg Equilibrium. Analysis of molecular variance (AMOVA) indicated that only 0.5% of the variation corresponded to differences among subpopulations, and 99.5% corresponded to differences among individuals. Factorial correspondence analysis showed intense admixtures across the putative subpopulations, and the subdivision related to geographical or environmental adaptation was undetectable. The Northern Morocco goat population presented high genetic diversity and a lack of population structure. The main reason for these findings is the absence of the breed concept (reproductively closed population), resulting in uncontrolled crossbreeding with exotic breeds and other local goats.

  15. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, caviidae in Colombia

    Directory of Open Access Journals (Sweden)

    William Burgos-Paz

    2011-01-01

    Full Text Available The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p < 0.05, genetic differentiation between population pairs was found to be low. Genetic distance, as well as clustering of guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

  16. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

    Science.gov (United States)

    Bickhart, Derek M.; Xu, Lingyang; Hutchison, Jana L.; Cole, John B.; Null, Daniel J.; Schroeder, Steven G.; Song, Jiuzhou; Garcia, Jose Fernando; Sonstegard, Tad S.; Van Tassell, Curtis P.; Schnabel, Robert D.; Taylor, Jeremy F.; Lewin, Harris A.; Liu, George E.

    2016-01-01

    The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. PMID:27085184

  17. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  18. DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK

    Science.gov (United States)

    The relationship between population adaptive potential and extinction risk in a changing environment is not well understood. Although the expectation is that genetic diversity is directly related to the capacity of populations to adapt, the statistical and predictive aspects of ...

  19. Genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The Ethiopian genetic center is considered to be one of the secondary centers of diversity for the common bean. This study was conducted to characterize the distribution of genetic diversity between and within ecological/geographical regions of Ethiopia. A germplasm sample of 116 landrace accessions was developed, ...

  20. Genetic diversity of Tamarindus indica populations: Any clues on the ...

    African Journals Online (AJOL)

    Tamarindus indica is a domesticated species of high economic value for the Sahel region. Despite this importance, very few data is available on its diversity as well as its structure leading to controversial discussions on its origin. Thus it is questionable whether the knowledge of its genetic diversity and organisation may ...

  1. Mitochondrial D-loop analysis for uncovering the population structure and genetic diversity among the indigenous duck (Anas platyrhynchos) populations of India.

    Science.gov (United States)

    Gaur, Uma; Tantia, Madhu Sudan; Mishra, Bina; Bharani Kumar, Settypalli Tirumala; Vijh, Ramesh Kumar; Chaudhury, Ashok

    2018-03-01

    The indigenous domestic duck (Anas platyrhynchos domestica) which is domesticated from Mallard (Anas platyrhynchos) contributes significantly to poor farming community in coastal and North Eastern regions of India. For conservation and maintenance of indigenous duck populations it is very important to know the existing genetic diversity and population structure. To unravel the population structure and genetic diversity among the five indigenous duck populations of India, the mitochondrial D-loop sequences of 120 ducks were analyzed. The sequence analysis by comparison of mtDNA D-loop region (470 bp) of five Indian duck populations revealed 25 mitochondrial haplotypes. Pairwise F ST value among populations was 0.4243 (p land birds revealed introgression of the out group breed Khaki Campbell, which is used for breed improvement programs in India. The observations revealed very less selection and a single matrilineal lineage of indigenous domestic ducks.

  2. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype and bacterial diversity (16S rDNA metabarcoding were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.

  3. Morpho-phenological diversity among natural populations of ...

    African Journals Online (AJOL)

    ... the high levels of within population variation and the lack of correlation between population differentiation and geographical distances suggest a potentially important rate of long-distance seed dispersal and confirm the role played by natural selection in the population structure of Tunisian populations of M. polymorpha.

  4. Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae) Population of the Araguaia-Tocantins Basin.

    Science.gov (United States)

    Vitorino, Carla A; Nogueira, Fabrícia; Souza, Issakar L; Araripe, Juliana; Venere, Paulo C

    2017-01-01

    The arapaima, Arapaima gigas , is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas , although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise F ST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise) may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin.

  5. The Relationship between Mating System and Genetic Diversity in Diploid Sexual Populations of Cyrtomium falcatum in Japan.

    Directory of Open Access Journals (Sweden)

    Ryosuke Imai

    Full Text Available The impact of variation in mating system on genetic diversity is a well-debated topic in evolutionary biology. The diploid sexual race of Cyrtomium falcatum (Japanese holly fern shows mating system variation, i.e., it displays two different types of sexual expression (gametangia formation in gametophytes: mixed (M type and separate (S type. We examined whether there is variation in the selfing rate among populations of this species, and evaluated the relationship between mating system, genetic diversity and effective population size using microsatellites. In this study, we developed eight new microsatellite markers and evaluated genetic diversity and structure of seven populations (four M-type and three S-type. Past effective population sizes (Ne were inferred using Approximate Bayesian computation (ABC. The values of fixation index (FIS, allelic richness (AR and gene diversity (h differed significantly between the M-type (FIS: 0.626, AR: 1.999, h: 0.152 and the S-type (FIS: 0.208, AR: 2.718, h: 0.367 populations (when admixed individuals were removed from two populations. Although evidence of past bottleneck events was detected in all populations by ABC, the current Ne of the M-type populations was about a third of that of the S-type populations. These results suggest that the M-type populations have experienced more frequent bottlenecks, which could be related to their higher colonization ability via gametophytic selfing. Although high population differentiation among populations was detected (FST = 0.581, F'ST = 0.739, there was no clear genetic differentiation between the M- and S-types. Instead, significant isolation by distance was detected among all populations. These results suggest that mating system variation in this species is generated by the selection for single spore colonization during local extinction and recolonization events and there is no genetic structure due to mating system.

  6. Therapeutic songwriting in music therapy, Part II: Comparing the literature with practice across diverse clinical populations

    DEFF Research Database (Denmark)

    Baker, Felicity; Wigram, Tony; Stott, Dave

    2009-01-01

      A growing body of literature on therapeutic songwriting with diverse clinical populations indicates that clinicians employ a wide range of approaches. The purpose of this research was to establish trends in the clinical practice of songwriting as implemented across a range of clinical populations....... Responses to a 21-question on-line survey were obtained from 419 professional music therapists practicing in 29 countries which focused on approaches to songwriting within their practice with a single clinical population. Results suggest that in general, the literature provides good representation for what...... is occurring in clinical practice. Generally, songs were composed with individual clients in single sessions, with lyrics created prior to the music. Clinicians had a significant role in creating the music with improvised and pre-determined musical structures being equally employed.  Chi-square or comparable...

  7. Epigenetic diversity increases the productivity and stability of plant populations

    Czech Academy of Sciences Publication Activity Database

    Latzel, Vít; Allan, E.; Bortolini Silveira, A.; Colot, V.; Fischer, M.; Bossdorf, O.

    2013-01-01

    Roč. 4, Nov 2013 (2013), s. 1-7, č. 2875 ISSN 2041-1723 Institutional support: RVO:67985939 Keywords : Arabidopsis thaliana * ecosystem * diversity Subject RIV: EF - Botanics Impact factor: 10.742, year: 2013

  8. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... polymorphic molecular markers for use in hybridization and variety development. Genomic ... The model-based cluster analysis of SSR diversity in the ...... clusters of individuals using the software STRUCTURE: A simulation.

  9. Downscaling Climate Science to the Classroom: Diverse Opportunities for Teaching Climate Science in Diverse Ways to Diverse Undergraduate Populations

    Science.gov (United States)

    Jones, R. M.; Gill, T. E.; Quesada, D.; Hedquist, B. C.

    2015-12-01

    Climate literacy and climate education are important topics in current socio-political debate. Despite numerous scientific findings supporting global climate changes and accelerated greenhouse warming, there is a social inertia resisting and slowing the rate at which many of our students understand and absorb these facts. A variety of reasons, including: socio-economic interests, political and ideological biases, misinformation from mass media, inappropriate preparation of science teachers, and lack of numancy have created serious challenges for public awareness of such an important issue. Different agencies and organizations (NASA, NOAA, EPA, AGU, APS, AMS and others) have created training programs for educators, not involved directly in climatology research, in order to learn climate science in a consistent way and then communicate it to the public and students. Different approaches on how to deliver such information to undergraduate students in diverse environments is discussed based on the author's experiences working in different minority-serving institutions across the nation and who have attended AMS Weather and Climate Studies training workshops, MSI-REACH, and the School of Ice. Different parameters are included in the analysis: demographics of students, size of the institutions, geographical locations, target audience, programs students are enrolled in, conceptual units covered, and availability of climate-related courses in the curricula. Additionally, the feasibility of incorporating a laboratory and quantitative analysis is analyzed. As a result of these comparisons it seems that downscaling of climate education experiences do not always work as expected in every institution regardless of the student body demographics. Different geographical areas, student body characteristics and type of institution determine the approach to be adopted as well as the feasibility to introduce different components for weather and climate studies. Some ideas are shared

  10. Significance of anaerobic bacteria in postoperative infection after radical cystectomy and urinary diversion or reconstruction.

    Science.gov (United States)

    Hiyama, Yoshiki; Takahashi, Satoshi; Uehara, Teruhisa; Hashimoto, Jiro; Kurimura, Yuichiro; Tanaka, Toshiaki; Masumori, Naoya; Tsukamoto, Taiji

    2013-10-01

    Radical cystectomy followed by urinary diversion or reconstruction (RC) is a standard treatment for patients with muscle-invasive bladder cancer. In these operations, a high frequency of complications, especially postoperative infection, has been reported. However, there have only been a few studies about postoperative anaerobic bacterial infection. To clarify the significance and role of anaerobic bacteria in postoperative infection, we retrospectively analyzed cases in which postoperative infection by these organisms developed. A total of 126 patients who underwent RC from 2006 to 2010 were included in this study. Various types of postoperative infection occurred in 66 patients. Anaerobic bacterial infections were detected with cultures for urine and blood in one case, for blood in two cases, and for surgical wound pus in four. The frequency of postoperative anaerobic bacterial infection in RC was less than that of colon surgery. However, this study revealed the possible development of a nonnegligible number of postoperative anaerobic bacterial infections. Therefore, we should consider anaerobic bacteria as possible pathogens in postoperative infection after RC.

  11. Sex expression and floral diversity in Jatropha curcas: a population study in its center of origin

    Science.gov (United States)

    Adriano-Anaya, María de Lourdes; Pérez-Castillo, Edilma; Salvador-Figueroa, Miguel; Ruiz-González, Sonia; Vázquez-Ovando, Alfredo; Grajales-Conesa, Julieta

    2016-01-01

    Sex expression and floral morphology studies are central to understand breeding behavior and to define the productive potential of plant genotypes. In particular, the new bioenergy crop Jatropha curcas L. has been classified as a monoecious species. Nonetheless, there is no information about its reproductive diversity in the Mesoamerican region, which is considered its center of origin and diversification. Thus, we determined sex expression and floral morphology in J. curcas populations from southern Mexico and Guatemala. Our results showed that most of J. curcas specimens had typical inflorescences with separate sexes (monoecious); meanwhile, the rest were atypical (gynoecious, androecious, andromonoecious, androgynomonoecious). The most important variables to group these populations, based on a discriminant analysis, were: male flower diameter, female petal length and male nectary length. From southern Mexico “Guerrero” was the most diverse population, and “Centro” had the highest variability among the populations from Chiapas. A cluster analysis showed that the accessions from southern Mexico were grouped without showing any correlation with the geographical origin, while those accessions with atypical sexuality were grouped together. To answer the question of how informative are floral morphological traits compared to molecular markers, we perform a Mantel correlation test between the distance matrix generated in this study and the genetic distance matrix (AFLP) previously reported for the same accessions. We found significant correlation between data at the level of accessions. Our results contribute to design genetic improvement programs by using sexually and morphologically contrasting plants from the center of origin. PMID:27257548

  12. Genetic diversity and population structure of the Guinea pig (Cavia porcellus, Rodentia, Caviidae) in Colombia.

    Science.gov (United States)

    Burgos-Paz, William; Cerón-Muñoz, Mario; Solarte-Portilla, Carlos

    2011-10-01

    The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allelic richness ranging from 3.0 to 6.56, and observed heterozygosity (Ho) from 0.33 to 0.60, with a deficit in heterozygous individuals. Although statistically significant (p guinea-pig lines and populations, coincided with the historical and geographical distribution of the populations. Likewise, high genetic identity between improved and native lines was established. An analysis of group probabilistic assignment revealed that each line should not be considered as a genetically homogeneous group. The findings corroborate the absorption of native genetic material into the improved line introduced into Colombia from Peru. It is necessary to establish conservation programs for native-line individuals in Nariño, and control genealogical and production records in order to reduce the inbreeding values in the populations.

  13. Patterns of genetic diversity and differentiation in the tsetse fly Glossina morsitans morsitans Westwood populations in East and southern Africa

    International Nuclear Information System (INIS)

    Ouma, J.O.; Marquez, J.G.; Krafsur, E.S

    2007-01-01

    Genetic diversity and differentiation within and among nine G. morsitans morsitans populations from East and southern Africa was assessed by examining variation at seven microsatellite loci and a mitochondrial locus, cytochrome oxidase (COI). Mean COI diversity within populations was 0.63 ± 0.33 and 0.81 taken over all populations. Diversities averaged over microsatellite loci were high (mean number of alleles/locus ≥7.4; mean HE ≥ 65%) in all populations. Diversities averaged across populations were greater in East Africa (mean number of alleles = 22 ± 2.6; mean he = 0.773 ± 0.033) than in southern Africa (mean number of alleles = 18.7 ± 4.0; mean he = 0.713 ± 0.072). Differentiation among all populations was highly significant (RST = 0.25, FST = 0.132). Nei’s Gij statistics were 0.09 and 0.19 within regions for microsatellites and mitochondria, respectively; between regions, Gij was 0.14 for microsatellites and 0.23 for mitochondria. GST among populations was 0.23 for microsatellite loci and 0.40 for mitochondria. The F, G and R statistics indicate highly restricted gene flow among G. m. morsitans populations separated over geographic scales of 12–917 km. (author)

  14. HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.

    Science.gov (United States)

    Maldarelli, Frank; Kearney, Mary; Palmer, Sarah; Stephens, Robert; Mican, JoAnn; Polis, Michael A; Davey, Richard T; Kovacs, Joseph; Shao, Wei; Rock-Kress, Diane; Metcalf, Julia A; Rehm, Catherine; Greer, Sarah E; Lucey, Daniel L; Danley, Kristen; Alter, Harvey; Mellors, John W; Coffin, John M

    2013-09-01

    HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.

  15. Diverse coupling of neurons to populations in sensory cortex.

    Science.gov (United States)

    Okun, Michael; Steinmetz, Nicholas; Cossell, Lee; Iacaruso, M Florencia; Ko, Ho; Barthó, Péter; Moore, Tirin; Hofer, Sonja B; Mrsic-Flogel, Thomas D; Carandini, Matteo; Harris, Kenneth D

    2015-05-28

    A large population of neurons can, in principle, produce an astronomical number of distinct firing patterns. In cortex, however, these patterns lie in a space of lower dimension, as if individual neurons were "obedient members of a huge orchestra". Here we use recordings from the visual cortex of mouse (Mus musculus) and monkey (Macaca mulatta) to investigate the relationship between individual neurons and the population, and to establish the underlying circuit mechanisms. We show that neighbouring neurons can differ in their coupling to the overall firing of the population, ranging from strongly coupled 'choristers' to weakly coupled 'soloists'. Population coupling is largely independent of sensory preferences, and it is a fixed cellular attribute, invariant to stimulus conditions. Neurons with high population coupling are more strongly affected by non-sensory behavioural variables such as motor intention. Population coupling reflects a causal relationship, predicting the response of a neuron to optogenetically driven increases in local activity. Moreover, population coupling indicates synaptic connectivity; the population coupling of a neuron, measured in vivo, predicted subsequent in vitro estimates of the number of synapses received from its neighbours. Finally, population coupling provides a compact summary of population activity; knowledge of the population couplings of n neurons predicts a substantial portion of their n(2) pairwise correlations. Population coupling therefore represents a novel, simple measure that characterizes the relationship of each neuron to a larger population, explaining seemingly complex network firing patterns in terms of basic circuit variables.

  16. Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management.

    Science.gov (United States)

    Wultsch, Claudia; Caragiulo, Anthony; Dias-Freedman, Isabela; Quigley, Howard; Rabinowitz, Salisa; Amato, George

    2016-01-01

    Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of

  17. Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species.

    Science.gov (United States)

    Nevado, B; Mautner, S; Sturmbauer, C; Verheyen, E

    2013-08-01

    Understanding how genetic variation is generated and maintained in natural populations, and how this process unfolds in a changing environment, remains a central issue in biological research. In this work, we analysed patterns of genetic diversity from several populations of three cichlid species from Lake Tanganyika in parallel, using the mitochondrial DNA control region. We sampled populations inhabiting the littoral rocky habitats in both very deep and very shallow areas of the lake. We hypothesized that the former would constitute relatively older, more stable and genetically more diverse populations, because they should have been less severely affected by the well-documented episodes of dramatic water-level fluctuations. In agreement with our predictions, populations of all three species sampled in very shallow shorelines showed traces of stronger population growth than populations of the same species inhabiting deep shorelines. However, contrary to our working hypothesis, we found a significant trend towards increased genetic diversity in the younger, demographically less stable populations inhabiting shallow areas, in comparison with the older and more stable populations inhabiting the deep shorelines. We interpret this finding as the result of the establishment of metapopulation dynamics in the former shorelines, by the frequent perturbation and reshuffling of individuals between populations due to the lake-level fluctuations. The repeated succession of periods of allopatric separation and secondary contact is likely to have further increased the rapid pace of speciation in lacustrine cichlids. © 2013 John Wiley & Sons Ltd.

  18. Gene diversity in some Muslim populations of North India.

    Science.gov (United States)

    Aarzoo, S Shabana; Afzal, Mohammad

    2005-06-01

    North Indian Muslim populations have historical, linguistic, and socioreligious significance to the Indian subcontinent. Although sociocultural and political dimensions of their demography are well documented, no detailed genetic structure of the populations is available. We have undertaken a survey of the gene frequencies of the ABO, Rh, PTC taste ability, sickling, and G6PD systems for different endogamous groups: Sheikh, Syed, Pathan, Ansari, Saifi, and Hindu Bania. All the groups at most loci showed statistically nonsignificant differences, except for ABO and PTC traits, for which interpopulational differences were seen. Heterozygosity ranged from 0.048 to 0.617 among the Sheikh, 0.149 to 0.599 among the Pathan, 0.105 to 0.585 among the Ansari, 0.25 to 0.869 among the Syed, 0.107 to 0.565 among the Saifi, and 0.100 to 0.492 among the Hindu Bania. The average D(ST) and G(ST) values for the five marker loci were 0.0625 +/- 0.098 and 0.1072 +/- 0.041, respectively. A dendrogram was constructed using the UPGMA clustering method. Our results revealed that the Pathan and the Sheikh form one cluster, the Syed and the Hindu Bania form another cluster, and the two clusters join together (the so-called higher caste); also, the Saifi and the Ansari form a separate cluster (lower caste). The results of the genetic distance analysis are useful for understanding the pattern of genetic relationships between different endogamous groups of Muslims.

  19. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  20. Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences.

    Science.gov (United States)

    Wu, Fengnian; Jiang, Hongyan; Beattie, G Andrew C; Holford, Paul; Chen, Jianchi; Wallis, Christopher M; Zheng, Zheng; Deng, Xiaoling; Cen, Yijing

    2018-04-24

    Diaphorina citri (Asian citrus psyllid; ACP) transmits 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this study, we evaluated ACP population diversity in China using representative whole mitochondrial genome (mitogenome) sequences. Additional mitogenome sequences outside China were also acquired and evaluated. The sizes of the 27 ACP mitogenome sequences ranged from 14 986 to 15 030 bp. Along with three previously published mitogenome sequences, the 30 sequences formed three major mitochondrial groups (MGs): MG1, present in southwestern China and occurring at elevations above 1000 m; MG2, present in southeastern China and Southeast Asia (Cambodia, Indonesia, Malaysia, and Vietnam) and occurring at elevations below 180 m; and MG3, present in the USA and Pakistan. Single nucleotide polymorphisms in five genes (cox2, atp8, nad3, nad1 and rrnL) contributed mostly in the ACP diversity. Among these genes, rrnL had the most variation. Mitogenome sequences analyses revealed two major phylogenetic groups of ACP present in China as well as a possible unique group present currently in Pakistan and the USA. The information could have significant implications for current ACP control and HLB management. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

  1. Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

    Science.gov (United States)

    Arnau, Gemma; MN, Sheela; Chair, Hana; Lebot, Vincent; K, Abraham; Perrier, Xavier; Petro, Dalila; Penet, Laurent; Pavis, Claudie

    2017-01-01

    Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods. PMID:28355293

  2. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy

    DEFF Research Database (Denmark)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert

    2014-01-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population...... structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild...... populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops...

  3. Analyses between Reproductive Behaviour, Genetic Diversity and Pythium Responsiveness in Zingiber spp. reveal an adaptive significance for hemiclonality

    Directory of Open Access Journals (Sweden)

    Geethu Elizabath Thomas

    2016-12-01

    Full Text Available AbstractMode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller’s ratchet. However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behaviour on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behaviour, amplified fragment length polymorphism (AFLP diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale. Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller’s ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behaviour. The populations inhabiting forest understory were large and

  4. Genomic patterns in Acropora cervicornis show extensive population structure and variable genetic diversity.

    Science.gov (United States)

    Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego

    2017-08-01

    Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.

  5. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: Implications for conservation

    Science.gov (United States)

    Huff, David D.; Miller, Loren M.; Vondracek, Bruce C.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.

  6. Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas L.

    Science.gov (United States)

    Martínez-Díaz, Yesenia; González-Rodríguez, Antonio; Rico-Ponce, Héctor Rómulo; Rocha-Ramírez, Víctor; Ovando-Medina, Isidro; Espinosa-García, Francisco J

    2017-01-01

    Jatropha curcas L. (Euphorbiaceae) is a shrub native to Mexico and Central America, which produces seeds with a high oil content that can be converted to biodiesel. The genetic diversity of this plant has been widely studied, but it is not known whether the diversity of the seed oil chemical composition correlates with neutral genetic diversity. The total seed oil content, the diversity of profiles of fatty acids and phorbol esters were quantified, also, the genetic diversity obtained from simple sequence repeats was analyzed in native populations of J. curcas in Mexico. Using the fatty acids profiles, a discriminant analysis recognized three groups of individuals according to geographical origin. Bayesian assignment analysis revealed two genetic groups, while the genetic structure of the populations could not be explained by isolation-by-distance. Genetic and fatty acid profile data were not correlated based on Mantel test. Also, phorbol ester content and genetic diversity were not associated. Multiple linear regression analysis showed that total oil content was associated with altitude and seasonality of temperature. The content of unsaturated fatty acids was associated with altitude. Therefore, the cultivation planning of J. curcas should take into account chemical variation related to environmental factors. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

  7. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    Directory of Open Access Journals (Sweden)

    Monika Sharma

    Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

  8. Genetic Diversity and Population Structure of Varronia curassavica: A Medicinal Polyploid Species in a Threatened Ecosystem.

    Science.gov (United States)

    Hoeltgebaum, Marcia Patricia; Dos Reis, Maurício Sedrez

    2017-06-01

    Varronia curassavica is an important medicinal species associated with the restinga, one of the most threatened coastal ecosystems of the Atlantic Forest. These circumstances call for studies aimed at estimating effective population size and gene flow to improve conservation efforts. Hence, the present study aimed to characterize the genetic diversity, ploidy level, and population structure of this species in different areas of restinga using microsatellites. Varronia curassavica was characterized as an autotetraploid, with high genetic variability, low divergence, and no significant fixation indices, indicating the absence of, or reduced, inbreeding and genetic drift in the study area. About 44% of the alleles occurred at low frequency in adults of all populations and 41% in the progenies evaluated. Gene flow was high, consistent with outcrossing species with high dispersal capacity (Nm = 4.87). The results showed no tendency toward isolation by distance. The estimated effective size indicates that the populations studied have the potential to ensure conservation of the species in the long term. The genetic variability and population structure of V. curassavica, as determined in this study, could form the foundation for activities directed toward the sustainable use of this resource and its conservation. Even though the restinga ecosystem has suffered dramatic reductions in area, this study provides evidence that this species is resilient to anthropogenic threats to its genetic integrity, since it is a polyploid with self-incompatibility mechanisms that contribute to maintaining high genetic diversity in an panmictic meta-population along the coast of Santa Catarina. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Molecular genetic diversity study of Lepidium sativum population ...

    African Journals Online (AJOL)

    Vostro 2520

    Generally, Tigray and Amhara regions showed moderate to high diversity in ISSR analysis. ... other crops. The main purpose of its cultivation in. Ethiopia is to use it as a medicinal plant. It is used for human abdominal ache and diarrhea. Moreover, L. ... of 10 primers were obtained from the Genetic Research Laboratory.

  10. Population genomics diversity of Plasmodium falciparum in malaria ...

    African Journals Online (AJOL)

    Background: Plasmodium falciparum, the most dangerous malaria parasite species to humans remains an important public health concern in Okelele, a rural community in Ilorin, Kwara State, Nigeria. There is however little information about the genetic diversity of Plasmodium falciparum in Nigeria. Objective: To determine ...

  11. Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

    Directory of Open Access Journals (Sweden)

    Sajjad Ahmad

    2015-06-01

    Full Text Available Field pea (Pisum sativum L. is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model (MLM taking population structure (Q and relative kinship (K into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

  12. Extrinsic factors significantly affect patterns of disease in free-ranging and captive cheetah (Acinonyx jubatus) populations.

    Science.gov (United States)

    Munson, Linda; Terio, Karen A; Worley, Michael; Jago, Mark; Bagot-Smith, Arthur; Marker, Laurie

    2005-07-01

    The cheetah (Acinonyx jubatus) has been considered a paradigm for disease vulnerability due to loss of genetic diversity. This species monomorphism has been suspected to be the basis for their general poor health and dwindling populations in captivity. North American and South African captive populations have high prevalences of hepatic veno-occlusive disease, glomerulosclerosis, gastritis, and systemic amyloidosis, diseases that are rare in other species. Unusually severe inflammatory reactions to common infectious agents have also been documented in captive cheetahs. The current study compared disease prevalences in free-ranging Namibian cheetahs with those in two captive populations of similar ages. The occurrence of diseases in the free-ranging population was determined from 49 necropsies and 27 gastric biopsies obtained between 1986 and 2003 and compared with prevalences in 147 North American and 80 South African captive cheetahs. Except for two cheetahs, the free-ranging population was in robust health with only mild lesions present, in contrast with significantly higher prevalences in the captive populations. Despite widespread heavy Helicobacter colonization in wild cheetahs, only 3% of the free-ranging population had moderate to severe gastritis, in contrast with 64% of captive cheetahs. No severe inflammatory reactions to viral infections were detected in the free-ranging animals. Because free-ranging Namibian cheetahs are as genetically impoverished as captive cheetahs, these findings caution against attributing loss of fitness solely to genetic factors and attest to the fundamental importance of extrinsic factors in wildlife health.

  13. Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians

    Directory of Open Access Journals (Sweden)

    Alicia S. Goicoechea

    2000-09-01

    Full Text Available Fertility, mortality and migration data from four Mapuche Indian communities located along a 215-km NE-SW linear area in the Province of Río Negro, Argentina, were collated with genetic information furnished by nine blood group systems and by mtDNA haplogroups. The demographic and genetic data indicated a clear dichotomy, which split the four populations into two groups of two. Differing degrees of non-Indian exchanges was probably the main determining factor for this separation. Total genetic variability was very similar in all groups, and the interpopulational variability accounted for only 10% of the total variability. A low prevalence of the Diego(a antigen among the Mapuche was confirmed. The fact that significant genetic heterogeneity and population clusters were found in such a small territorial region attests to the sensitivity of demographic and genetic approaches in unraveling human history.Dados relativos a fertilidade, mortalidade e migração de quatro comunidades de índios Mapuche localizadas em uma área linear na direção nordeste-sudoeste com 215 km de extensão na Província de Rio Negro, Argentina, foram associados com a informação genética fornecida por nove sistemas de grupos sangüíneos e os haplogrupos do DNA mitocondrial. Ambos os tipos de informação apontam claramente para uma dicotomia, as quatro populações sendo divididas em grupos de duas. O principal fator responsável por esta separação é provavelmente graus diferentes de mistura com não-índios. A variabilidade genética total foi muito similar em todos os grupos, aquela entre populações sendo de apenas 10% deste valor. Foi confirmada a baixa prevalência do antígeno Diego(a entre os Mapuche. O fato de que heterogeneidade genética significativa e conjuntos populacionais diversos foram observados em uma região territorial tão pequena demonstra a sensibilidade dos enfoques demográfico e genético no esclarecimento da história humana.

  14. Analysis of genetic diversity and population structure among exotic ...

    African Journals Online (AJOL)

    The same clustering pattern was also found in the PCoA analysis. In all the geographical populations, genotypes from the same country were often in different clusters and likewise accessions from different countries often clustered together indicating the possibility of exchange of materials between countries. Population ...

  15. Evolution of increased phenotypic diversity enhances population performance by reducing sexual harassment in damselflies.

    Science.gov (United States)

    Takahashi, Yuma; Kagawa, Kotaro; Svensson, Erik I; Kawata, Masakado

    2014-07-18

    The effect of evolutionary changes in traits and phenotypic/genetic diversity on ecological dynamics has received much theoretical attention; however, the mechanisms and ecological consequences are usually unknown. Female-limited colour polymorphism in damselflies is a counter-adaptation to male mating harassment, and thus, is expected to alter population dynamics through relaxing sexual conflict. Here we show the side effect of the evolution of female morph diversity on population performance (for example, population productivity and sustainability) in damselflies. Our theoretical model incorporating key features of the sexual interaction predicts that the evolution of increased phenotypic diversity will reduce overall fitness costs to females from sexual conflict, which in turn will increase productivity, density and stability of a population. Field data and mesocosm experiments support these model predictions. Our study suggests that increased phenotypic diversity can enhance population performance that can potentially reduce extinction rates and thereby influence macroevolutionary processes.

  16. Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

    DEFF Research Database (Denmark)

    Miller, Webb; Hayes, Vanessa M.; Ratan, Aakrosh

    2011-01-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. The inability to mount an immune response and to reject these tumors might be caused by a lack of genetic diversity within a dwindling population. Here we...... that the observed low genetic diversity in today's population preceded the Devil Facial Tumor Disease disease outbreak by at least 100 y. Using a genetically characterized breeding stock based on the genome sequence will enable preservation of the extant genetic diversity in future Tasmanian devil populations....

  17. Genetic diversity in Chilean populations of rainbow trout, Oncorhynchus mykiss

    Directory of Open Access Journals (Sweden)

    Claudia B Cárcamo

    2015-03-01

    Full Text Available The rainbow trout Oncorhynchus mykiss, was first introduced in Chile between 1905 and 1920 and is currently widely distributed in Chile from Antofagasta (23°S to Patagonia (55°S. The broad range of the geographic and climatic distributions of this species in Chile offers a unique opportunity to study the effect of naturalization of an introduced species on its genetic variability. It is of particular importance to observe the genetic variability of populations in the northern range of this species distribution, in a transition zone where a Mediterranean-type climate changes to an arid climate. The present study analyzed allozymic variability and distribution within and between populations of O. mykiss from the river basins of Elqui and Limari rivers, and six culture strains, using starch-gel protein electrophoresis. Populations were found to be in Hardy-Weinberg equilibrium and the average values of He (0.045, polymorphism (13.9% and allele per locus (1.19 are similar to rainbow trout in its native distributional range. About 77.8% of the genetic variability was within population, similar to the variability reported for wild populations in the northern hemisphere. However, a marked genetic differentiation between wild populations was also found. This is likely to be the consequence of initial founder effects followed by subsequent introgression of resident populations caused by reseeding with trout of different origins in both basins.

  18. Characteristics of phylogenetic diversity in airborne bacterial populations in China

    Science.gov (United States)

    Chaudhry, Zahra; Santarpia, Joshua L.; Martins, J. V.

    2011-05-01

    Considering their potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known about the composition or dynamics of the atmosphere's biological aerosols. The few studies that have examined phylogenetic diversity in China focused on a single sampling period, whereas this study spans 3 months and includes over 300 samples. The 300+ samples were categorized by month and direction of their back-trajectory. DNA extraction was carried out on the pooled samples in a quantitative manner to allow for comparison between the amount of extracted material and the amount of initial total aerosol mass. Within an individual month, samples originating from similar land types and approximately equidistant to the sampling location exhibited similar diversity, whereas samples originating from much greater distances and from different land types included phyla unique to that location. Phyla from the same origin also varied from one month to the next. The biological diversity found from the Phylochips reinforces the hypothesis that air samples carry a biological record of their history.

  19. Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

    Science.gov (United States)

    Sun, Xinxu; Xu, Dongdong; Lou, Bao; Zhang, Tao; Xin, Jian; Guo, Yaoshi; Ma, Shilei

    2013-11-01

    Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity ( h =0.759±0.035) and low levels of nucleotide diversity ( π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant ( φ st=0.032 85, PTests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

  20. Diversity and Genetic Variation among Brevipalpus Populations from Brazil and Mexico

    Science.gov (United States)

    Sánchez-Velázquez, E. J.; Santillán-Galicia, M. T.; Novelli, V. M.; Nunes, M. A.; Mora-Aguilera, G.; Valdez-Carrasco, J. M.; Otero-Colina, G.; Freitas-Astúa, J.

    2015-01-01

    Brevipalpus phoenicis s.l. is an economically important vector of the Citrus leprosis virus-C (CiLV-C), one of the most severe diseases attacking citrus orchards worldwide. Effective control strategies for this mite should be designed based on basic information including its population structure, and particularly the factors that influence its dynamics. We sampled sweet orange orchards extensively in eight locations in Brazil and 12 in Mexico. Population genetic structure and genetic variation between both countries, among locations and among sampling sites within locations were evaluated by analysing nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). In both countries, B. yothersi was the most common species and was found in almost all locations. Individuals from B. papayensis were found in two locations in Brazil. Brevipalpus yothersi populations collected in Brazil were more genetically diverse (14 haplotypes) than Mexican populations (four haplotypes). Although geographical origin had a low but significant effect (ca. 25%) on the population structure, the greatest effect was from the within location comparison (37.02 %). Potential factors driving our results were discussed. PMID:26207373

  1. Morpho-phenological diversity among natural populations of ...

    African Journals Online (AJOL)

    sunny t

    populations (Badri et al., 2007, 2010; Arraouadi et al.,. 2009; Lazrek et al., 2009) were measured for the lines of. M. polymorpha. ..... an organism (Holderegger et al., 2006). Adaptation .... Mouradov A, Cremer F, Coupland G (2002). Control of ...

  2. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... ... Aromatic and Economic Plants, CSIR - North-East Institute of Science and Technology ... and population structure is receiving tremendous attention for effective .... unreliable detection and to increase the quality of data. The.

  3. Inter-populations genetic and morphological diversity in three Silene ...

    African Journals Online (AJOL)

    enoho

    2012-03-30

    Mar 30, 2012 ... 2Biology Department, School of Basic Sciences, Science and Research Branch, Islamic Azad University (SRBIAU), ... other populations in both morphological and molecular features. ... species with world-wide distribution.

  4. Diversity of human small intestinal Streptococcus and Veillonella populations

    NARCIS (Netherlands)

    van den Bogert, Bartholomeus; Erkus, Oylum; Boekhorst, Jos; de Goffau, Marcus; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

    Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed

  5. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy.

    Science.gov (United States)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert; Branca, Ferdinando; Bagger Jørgensen, Rikke

    2014-12-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops. It was possible to detect inter-crossing between leafy kales and B. rupestris. Findings from this study illustrate the existing level of genetic diversity in the B. oleracea gene pool. Individual populations (either wild or leafy kales) with higher levels of genetic diversity have been identified and suggestions are given for an informed conservation strategy. Domestication hypotheses are also discussed. © 2015 The Authors.

  6. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    Science.gov (United States)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  7. King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times.

    Science.gov (United States)

    Heupink, Tim H; van den Hoff, John; Lambert, David M

    2012-08-23

    Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.

  8. Significant biochemical, biophysical and metabolic diversity in circulating human cord blood reticulocytes.

    Directory of Open Access Journals (Sweden)

    Benoît Malleret

    Full Text Available The transition from enucleated reticulocytes to mature normocytes is marked by substantial remodeling of the erythrocytic cytoplasm and membrane. Despite conspicuous changes, most studies describe the maturing reticulocyte as a homogenous erythropoietic cell type. While reticulocyte staging based on fluorescent RNA stains such as thiazole orange have been useful in a clinical setting; these 'sub-vital' stains may confound delicate studies on reticulocyte biology and may preclude their use in heamoparasite invasion studies.Here we use highly purified populations of reticulocytes isolated from cord blood, sorted by flow cytometry into four sequential subpopulations based on transferrin receptor (CD71 expression: CD71high, CD71medium, CD71low and CD71negative. Each of these subgroups was phenotyped in terms of their, morphology, membrane antigens, biomechanical properties and metabolomic profile.Superficially CD71high and CD71medium reticulocytes share a similar gross morphology (large and multilobular when compared to the smaller, smooth and increasingly concave reticulocytes as seen in the in the CD71low and CD71negativesamples. However, between each of the four sample sets we observe significant decreases in shear modulus, cytoadhesive capacity, erythroid receptor expression (CD44, CD55, CD147, CD235R, and CD242 and metabolite concentrations. Interestingly increasing amounts of boric acid was found in the mature reticulocytes.Reticulocyte maturation is a dynamic and continuous process, confounding efforts to rigidly classify them. Certainly this study does not offer an alternative classification strategy; instead we used a nondestructive sampling method to examine key phenotypic changes of in reticulocytes. Our study emphasizes a need to focus greater attention on reticulocyte biology.

  9. Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

    Science.gov (United States)

    Herrera, C M; Pozo, M I; Bazaga, P

    2011-11-01

    Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

  10. Food Addiction: Its Prevalence and Significant Association with Obesity in the General Population

    OpenAIRE

    Pedram, Pardis; Wadden, Danny; Amini, Peyvand; Gulliver, Wayne; Randell, Edward; Cahill, Farrell; Vasdev, Sudesh; Goodridge, Alan; Carter, Jacqueline C.; Zhai, Guangju; Ji, Yunqi; Sun, Guang

    2013-01-01

    Background ?Food addiction? shares a similar neurobiological and behavioral framework with substance addiction. However whether, and to what degree, ?food addiction? contributes to obesity in the general population is unknown. Objectives to assess 1) the prevalence of ?food addiction? in the Newfoundland population; 2) if clinical symptom counts of ?food addiction? were significantly correlated with the body composition measurements; 3) if food addicts were significantly more obese than contr...

  11. Genetic Diversity, Population Structure, and Heritability of Fruit Traits in Capsicum annuum

    Science.gov (United States)

    Naegele, Rachel P.; Mitchell, Jenna; Hausbeck, Mary K.

    2016-01-01

    Cultivated pepper (Capsicum annuum) is a phenotypically diverse species grown throughout the world. Wild and landrace peppers are typically small-fruited and pungent, but contain many important traits such as insect and disease resistance. Cultivated peppers vary dramatically in size, shape, pungency, and color, and often lack resistance traits. Fruit characteristics (e.g. shape and pericarp thickness) are major determinants for cultivar selection, and their association with disease susceptibility can reduce breeding efficacy. This study evaluated a diverse collection of peppers for mature fruit phenotypic traits, correlation among fruit traits and Phytophthora fruit rot resistance, genetic diversity, population structure, and trait broad sense heritability. Significant differences within all fruit phenotype categories were detected among pepper lines. Fruit from Europe had the thickest pericarp, and fruit from Ecuador had the thinnest. For fruit shape index, fruit from Africa had the highest index, while fruit from Europe had the lowest. Five genetic clusters were detected in the pepper population and were significantly associated with fruit thickness, end shape, and fruit shape index. The genetic differentiation between clusters ranged from little to very great differentiation when grouped by the predefined categories. Broad sense heritability for fruit traits ranged from 0.56 (shoulder height) to 0.98 (pericarp thickness). When correlations among fruit phenotypes and fruit disease were evaluated, fruit shape index was negatively correlated with pericarp thickness, and positively correlated with fruit perimeter. Pepper fruit pericarp, perimeter, and width had a slight positive correlation with Phytophthora fruit rot, whereas fruit shape index had a slight negative correlation. PMID:27415818

  12. Enclaves of genetic diversity resisted Inca impacts on population history.

    Science.gov (United States)

    Barbieri, Chiara; Sandoval, José R; Valqui, Jairo; Shimelman, Aviva; Ziemendorff, Stefan; Schröder, Roland; Geppert, Maria; Roewer, Lutz; Gray, Russell; Stoneking, Mark; Fujita, Ricardo; Heggarty, Paul

    2017-12-12

    The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.

  13. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline; Ho, Shwen; Pires, Inê s S.; Tester, Mark A.; Negrã o, Só nia; Schmö cke, Sandra M.

    2017-01-01

    with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through

  14. Species Diversity of Oak Stands and Its Significance for Drought Resistance

    Directory of Open Access Journals (Sweden)

    Jan Kotlarz

    2018-03-01

    Full Text Available Drought periods have an adverse impact on the condition of oak stands. Research on different types of ecosystems has confirmed a correlation between plant species diversity and the adverse effects of droughts. The purpose of this study was to investigate the changes that occurred in an oak stand (Krotoszyn Plateau, Poland under the impact of the summer drought in 2015. We used a method based on remote sensing indices from satellite images in order to detect changes in the vegetation in 2014 and 2015. A positive difference was interpreted as an improvement, whereas a negative one was treated as a deterioration of the stand condition. The Shannon-Wiener species diversity was estimated using an iterative principal component analysis (PCA algorithm based on aerial images. We observed a relationship between the species indices of the individual forest divisions and their response to drought. The highest correlation between the index differences and the Shannon-Wiener indices was found for the Green Normalized Difference Vegetation Index (GNDVI index (+0.74. In addition, correlations were observed between the mean index difference and the percentage shares in the forest divisions of species such as Pinus sylvestris L. (P. sylvestris (+0.67 ± 0.08 and Quercus robur L. (Q. robur (−0.65 ± 0.10. Our results lead us to infer that forest management based on highly diverse habitats is more suitable to meet the challenges in the context of global climatic changes, characterized by increasingly frequent droughts.

  15. Past climate-driven range shifts and population genetic diversity in arctic plants

    DEFF Research Database (Denmark)

    Pellissier, Loïc; Eidesen, Pernille Bronken; Ehrich, Dorothee

    2016-01-01

    High intra-specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since ...... the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses...

  16. Mitochondrial genome diversity and population structure of the giant squid Architeuthis

    DEFF Research Database (Denmark)

    Winkelmann, Inger Eleanor Hall; Campos, Paula; Strugnell, Jan

    2013-01-01

    techniques, considerable controversy exists with regard to topics as varied as their taxonomy, biology and even behaviour. In this study, we have characterized the mitochondrial genome (mitogenome) diversity of 43 Architeuthis samples collected from across the range of the species, in order to use genetic...... a recent population expansion or selective sweep, which may explain the low level of genetic diversity....

  17. Relationships among walleye population characteristics and genetic diversity in northern Wisconsin Lakes

    Science.gov (United States)

    Waterhouse, Matthew D.; Sloss, Brian L.; Isermann, Daniel A.

    2014-01-01

    The maintenance of genetic integrity is an important goal of fisheries management, yet little is known regarding the effects of management actions (e.g., stocking, harvest regulations) on the genetic diversity of many important fish species. Furthermore, relationships between population characteristics and genetic diversity remain poorly understood. We examined relationships among population demographics (abundance, recruitment, sex ratio, and mean age of the breeding population), stocking intensity, and genetic characteristics (heterozygosity, effective number of alleles, allelic richness, Wright's inbreeding coefficient, effective population size [Ne], mean d2 [a measure of inbreeding], mean relatedness, and pairwise population ΦST estimates) for 15 populations of Walleye Sander vitreus in northern Wisconsin. We also tested for potential demographic and genetic influences on Walleye body condition and early growth. Combinations of demographic variables explained 47.1–79.8% of the variation in genetic diversity. Skewed sex ratios contributed to a reduction in Ne and subsequent increases in genetic drift and relatedness among individuals within populations; these factors were correlated to reductions in allelic richness and early growth rate. Levels of inbreeding were negatively related to both age-0 abundance and mean age, suggesting Ne was influenced by recruitment and generational overlap. A negative relationship between the effective number of alleles and body condition suggests stocking affected underlying genetic diversity of recipient populations and the overall productivity of the population. These relationships may result from poor performance of stocked fish, outbreeding depression, or density-dependent factors. An isolation-by-distance pattern of genetic diversity was apparent in nonstocked populations, but was disrupted in stocked populations, suggesting that stocking affected genetic structure. Overall, demographic factors were related to genetic

  18. Diversity and abundance of lepidopteran populations from selected crops of district faisalabad, pakistan

    International Nuclear Information System (INIS)

    Maalik, S.; Rana, S.A.; Khan, H.A.; Ashfaq, M.

    2012-01-01

    Lepidopterans are represented by one of the most diverse group of insects. They are phytophagous as well as pollinators at the same time. During present study four crops i.e Wheat, Fodder, Brassica and Vegetables were sampled to assess the diversity and abundance of Lepidopteran populations. A total of 2811 specimens belonging to 14 species and 6 families were recorded. Pieris brassicae (29.46%) was the dominant species followed by Trichoplusia ni (19.28%), Helicoverpa Zea (11.78%), Helicoverpa armigera (11.60%), Spodoptera exigua (6.65%), Psedoplusia includes (5.09%), Spodoptera litura (3.81%), Agrotis ipsilon (4.87%), Plutella xylostella (2.92%), Lymatria dispar (2.24%), Pieris rapae (0.92%), Galleria mellonella (0.71%), Evergestris rimosalis (0.53%) and Menduca sexta (0.14%). Significant differences were observed among different crops by applying Shannon Diversity Index and T- test. CA (Cluster analysis) represented the species association with different crops. Majority of the species showed association with Vegetables and Fodder and least association was observed with Wheat. Such types of studies are necessary to design integrated pest management programs to control these pests. (author)

  19. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers

    OpenAIRE

    Rocío Toledo-Aguilar; Higinio López-Sánchez; Amalio Santacruz-Varela; Ernestina Valadez-Moctezuma; Pedro A López; Víctor H Aguilar-Rincón; Víctor A González-Hernández; Humberto Vaquera-Huerta

    2016-01-01

    'Ancho' type chilis (Capsicum annuum L. var. annuum) are an important ingredient in the traditional cuisine of Mexico and so are in high demand. It includes six native sub-types with morphological and fruit color differences. However, the genetic diversity of the set of these sub­types has not been determined. The objective of this study was to characterize the genetic diversity of native Mexican ancho chili populations using microsatellites and to determine the relationship among these popul...

  20. Evolution of sociality in spiders leads to depleted genomic diversity at both population and species levels.

    Science.gov (United States)

    Settepani, V; Schou, M F; Greve, M; Grinsted, L; Bechsgaard, J; Bilde, T

    2017-08-01

    Across several animal taxa, the evolution of sociality involves a suite of characteristics, a "social syndrome," that includes cooperative breeding, reproductive skew, primary female-biased sex ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change. To investigate the consequences of this social life form on genetic diversity, we used a comparative RAD-sequencing approach to estimate genomewide diversity in spider species that differ in level of sociality, reproductive skew and mating system. We analysed multiple populations of three independent sister-species pairs of social inbreeding and subsocial outcrossing Stegodyphus spiders, and a subsocial outgroup. Heterozygosity and within-population diversity were sixfold to 10-fold lower in social compared to subsocial species, and demographic modelling revealed a tenfold reduction in Ne of social populations. Species-wide genetic diversity depends on population divergence and the viability of genetic lineages. Population genomic patterns were consistent with high lineage turnover, which homogenizes the genetic structure that builds up between inbreeding populations, ultimately depleting genetic diversity at the species level. Indeed, species-wide genetic diversity of social species was 5-8 times lower than that of subsocial species. The repeated evolution of species with this social syndrome is associated with severe loss of genomewide diversity, likely to limit their evolutionary potential. © 2017 John Wiley & Sons Ltd.

  1. Spatial distribution of genetic diversity in populations of Hagenia abyssinica (Bruce J.F. Gmel from Ethiopia

    Directory of Open Access Journals (Sweden)

    Taye Bekele Ayele

    2017-07-01

    Full Text Available Genetic variation among 596 individuals from 22 natural and 3 planted populations of Hagenia abyssinica (Rosaceae sampled from the montane forests of Ethiopia was investigated at amplified fragment length polymorphism (AFLP loci. We observed 106 unequivocally scorable AFLP markers out of which 91.5 percent were polymorphic. Populations harbored varying genetic diversities (He = 0.139-0.362, and showed low but significant genetic differentiation among them (FST = 0.077. Significant differentiation was observed even though previous paleoecological studies indicated that Hagenia abyssinica recolonized Ethiopia only after the Last Glacial Maximum, and our earlier analyses of maternally inherited chloroplast DNA revealed low mixing of recolonizing lineages through seeds and rare long distance seed dispersal. Genetic diversity did not decrease along recolonization routes, confirming effective gene flow, most likely through pollen, among populations. The observed variation at putatively neutral AFLPs does not reflect clinal variation patterns. As expected, population differentiation is lower at anonymous, mostly biparentally inherited, AFLPs than at maternally inherited chloroplast haplotypes. Despite presumably efficient seed and pollen dispersal of H. abyssinica by wind, a significant non-random fine-scale spatial genetic structure was observed up to 80 m in some populations. Due to significant pair-wise differentiation observed between populations, as many populations as possible should be considered for conservation, tree improvement and forestation programs.

  2. Genetic diversity of Ghanaian local chicken populations based on ...

    African Journals Online (AJOL)

    In Ghana, local chickens are raised across distinct agro-ecological zones and constitute unique populations with variable phenotypes that need to be characterized to provide needed information for the conservation of useful genotypes against future needs. In particular, the Interior Savannah (GHIS) in the north, the Forest ...

  3. Directional dominance on stature and cognition in diverse human populations

    NARCIS (Netherlands)

    Joshi, Peter K.; Esko, Tonu; Mattsson, Hannele; Eklund, Niina; Gandin, Ilaria; Nutile, Teresa; Jackson, Anne U.; Schurmann, Claudia; Smith, Albert V.; Zhang, Weihua; Okada, Yukinori; Stancakova, Alena; Faul, Jessica D.; Zhao, Wei; Bartz, Traci M.; Concas, Maria Pina; Franceschini, Nora; Enroth, Stefan; Vitart, Veronique; Trompet, Stella; Guo, Xiuqing; Chasman, Daniel I.; O'Connel, Jeffrey R.; Corre, Tanguy; Nongmaithem, Suraj S.; Chen, Yuning; Mangino, Massimo; Ruggiero, Daniela; Traglia, Michela; Farmaki, Aliki-Eleni; Kacprowski, Tim; Bjonnes, Andrew; van der Spek, Ashley; Wu, Ying; Giri, Anil K.; Yanek, Lisa R.; Wang, Lihua; Hofer, Edith; Rietveld, Cornelius A.; McLeod, Olga; Cornelis, Marilyn C.; Pattaro, Cristian; Verweij, Niek; Baumbach, Clemens; Abdellaoui, Abdel; Warren, Helen R.; Vuckovic, Dragana; Mei, Hao; Bouchard, Claude; Perry, John R. B.; Cappellani, Stefania; Mirza, Saira S.; Benton, Miles C.; Broeckel, Ulrich; Medland, Sarah E.; Lind, PenelopeA.; Malerba, Giovanni; Drong, Alexander; Yengo, Loic; Bielak, Lawrence F.; Zhi, Degui; van der Most, Peter J.; Shriner, Daniel; Maegi, Reedik; Hemani, Gibran; Karaderi, Tugce; Wang, Zhaoming; Liu, Tian; Demuth, Ilja; Zhao, Jing Hua; Meng, Weihua; Lataniotis, Lazaros; van der Laan, Sander W.; Bradfield, Jonathan P.; Wood, Andrew R.; Bonnefond, Amelie; Ahluwalia, Tarunveer S.; Hall, LeanneM.; Salvi, Erika; Yazar, Seyhan; Carstensen, Lisbeth; de Haan, Hugoline G.; Abney, Mark; Afzal, Uzma; Allison, Matthew A.; Amin, Najaf; Asselbergs, Folkert W.; Bakker, Stephan J. L.; Barr, R. Graham; Baumeister, Sebastian E.; Benjamin, Daniel J.; Bergmann, Sven; Boerwinkle, Eric; Bottinger, Erwin P.; Campbell, Archie; Chakravarti, Aravinda; Chan, Yingleong; Chanock, Stephen J.; Chen, Constance; Chen, Y. -D. Ida; Collins, Francis S.; Connell, John; Correa, Adolfo; Cupples, L. Adrienne; Smith, George Davey; Davies, Gail; Doerr, Marcus; Ehret, Georg; Ellis, Stephen B.; Feenstra, Bjarke; Feitosa, Mary F.; Ford, Ian; Fox, Caroline S.; Frayling, Timothy M.; Friedrich, Nele; Geller, Frank; Scotland, Generation; Gillham-Nasenya, Irina; Gottesman, Omri; Graff, Misa; Grodstein, Francine; Gu, Charles; Haley, Chris; Hammond, Christopher J.; Harris, Sarah E.; Harris, Tamara B.; Hastie, Nicholas D.; Heard-Costa, Nancy L.; Heikkila, Kauko; Hocking, Lynne J.; Homuth, Georg; Hottenga, Jouke-Jan; Huang, Jinyan; Huffman, Jennifer E.; Hysi, Pirro G.; Ikram, M. Arfan; Ingelsson, Erik; Joensuu, Anni; Johansson, Asa; Jousilahti, Pekka; Jukema, J. Wouter; Kahonen, Mika; Kamatani, Yoichiro; Kanoni, Stavroula; Kerr, Shona M.; Khan, Nazir M.; Koellinger, Philipp; Koistinen, Heikki A.; Kooner, Manraj K.; Kubo, Michiaki; Kuusisto, Johanna; Lahti, Jari; Launer, Lenore J.; Lea, Rodney A.; Lehne, Benjamin; Lehtimaki, Terho; Liewald, David C. M.; Lind, Lars; Loh, Marie; Lokki, Marja-Liisa; London, Stephanie J.; Loomis, Stephanie J.; Loukola, Anu; Lu, Yingchang; Lumley, Thomas; Lundqvist, Annamari; Mannisto, Satu; Marques-Vidal, Pedro; Masciullo, Corrado; Matchan, Angela; Mathias, Rasika A.; Matsuda, Koichi; Meigs, James B.; Meisinger, Christa; Meitinger, Thomas; Menni, Cristina; Mentch, Frank D.; Mihailov, Evelin; Milani, Lili; Montasser, May E.; Montgomery, GrantW.; Morrison, Alanna; Myers, Richard H.; Nadukuru, Rajiv; Navarro, Pau; Nelis, Mari; Nieminen, Markku S.; Nolte, Ilja M.; O'Connor, George T.; Ogunniyi, Adesola; Padmanabhan, Sandosh; Palmas, Walter R.; Pankow, James S.; Patarcic, Inga; Pavani, Francesca; Peyser, Patricia A.; Pietilainen, Kirsi; Poulter, Neil; Prokopenko, Inga; Ralhan, Sarju; Redmond, Paul; Rich, Stephen S.; Rissanen, Harri; Robino, Antonietta; Rose, Lynda M.; Rose, Richard; Sala, Cinzia; Salako, Babatunde; Salomaa, Veikko; Sarin, Antti-Pekka; Saxena, Richa; Schmidt, Helena; Scott, Laura J.; Scott, William R.; Sennblad, Bengt; Seshadri, Sudha; Sever, Peter; Shrestha, Smeeta; Smith, Blair H.; Smith, Jennifer A.; Soranzo, Nicole; Sotoodehnia, Nona; Southam, Lorraine; Stanton, Alice V.; Stathopoulou, Maria G.; Strauch, Konstantin; Strawbridge, Rona J.; Suderman, Matthew J.; Tandon, Nikhil; Tang, Sian-Tsun; Taylor, Kent D.; Tayo, Bamidele O.; Toeglhofer, Anna Maria; Tomaszewski, Maciej; Tsernikova, Natalia; Tuomilehto, Jaakko; Uitterlinden, Andre G.; Vaidya, Dhananjay; Vlieg, Astrid van Hylckama; van Setten, Jessica; Vasankari, Tuula; Vedantam, Sailaja; Vlachopoulou, Efthymia; Vozzi, Diego; Vuoksimaa, Eero; Waldenberger, Melanie; Ware, Erin B.; Wentworth-Shields, William; Whitfield, John B.; Wild, Sarah; Willemsen, Gonneke; Yajnik, Chittaranjan S.; Yao, Jie; Zaza, Gianluigi; Zhu, Xiaofeng; Salem, Rany M.; Melbye, Mads; Bisgaard, Hans; Samani, Nilesh J.; Cusi, Daniele; Mackey, David A.; Cooper, Richard S.; Froguel, Philippe; Pasterkamp, Gerard; Grant, Struan F. A.; Hakonarson, Hakon; Ferrucci, Luigi; Scott, Robert A.; Morris, Andrew D.; Palmer, Colin N. A.; Dedoussis, George; Deloukas, Panos; Bertram, Lars; Lindenberger, Ulman; Berndt, Sonja I.; Lindgren, Cecilia M.; Timpson, Nicholas J.; Toenjes, Anke; Munroe, Patricia B.; Sorensen, Thorkild I. A.; Rotimi, Charles N.; Arnett, Donna K.; Oldehinkel, Albertine J.; Kardia, Sharon L. R.; Balkau, Beverley; Gambaro, Giovanni; Morris, Andrew P.; Eriksson, Johan G.; Wright, Margie J.; Martin, Nicholas G.; Hunt, Steven C.; Starr, John M.; Deary, Ian J.; Griffiths, Lyn R.; Tiemeier, Henning; Pirastu, Nicola; Kaprio, Jaakko; Wareham, Nicholas J.; Perusse, Louis; Wilson, James G.; Girotto, Giorgia; Caulfield, Mark J.; Raitakari, Olli; Boomsma, Dorret I.; Gieger, Christian; van der Harst, Pim; Hicks, Andrew A.; Kraft, Peter; Sinisalo, Juha; Knekt, Paul; Johannesson, Magnus; Magnusson, Patrik K. E.; Hamsten, Anders; Schmidt, Reinhold; Borecki, Ingrid B.; Vartiainen, Erkki; Becker, Diane M.; Bharadwaj, Dwaipayan; Mohlke, Karen L.; Boehnke, Michael; van Duijn, Cornelia M.; Sanghera, Dharambir K.; Teumer, Alexander; Zeggini, Eleftheria; Metspalu, Andres; Gasparini, Paolo; Ulivi, Sheila; Ober, Carole; Toniolo, Daniela; Rudan, Igor; Porteous, David J.; Ciullo, Marina; Spector, Tim D.; Hayward, Caroline; Dupuis, Josee; Loos, Ruth J. F.; Wright, Alan F.; Chandak, Giriraj R.; Vollenweider, Peter; Shuldiner, Alan R.; Ridker, Paul M.; Rotter, Jerome I.; Sattar, Naveed; Gyllensten, Ulf; North, Kari E.; Pirastu, Mario; Psaty, Bruce M.; Weir, David R.; Laakso, Markku; Gudnason, Vilmundur; Takahashi, Atsushi; Chambers, John C.; Kooner, Jaspal S.; Strachan, David P.; Campbell, Harry; Hirschhorn, Joel N.; Perola, Markus; Polasek, Ozren; Wilson, James F.

    2015-01-01

    Homozygosity has long been associated with rare, often devastating, Mendelian disorders(1), and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness(2). However, the effect of the more distant parental relatedness that is common in modern human populations is less

  4. Genetic diversity and population structure of 10 Chinese indigenous ...

    Indian Academy of Sciences (India)

    This program uses a Monte Carlo Markov chain. (MCMC) algorithm to ... tal population, measured as FST value, for the 29 loci var- ied from 0.002 (SMO11) to .... linked to loci affecting morphological, productive or adap- tive traits of selective ...

  5. Genetic diversity of Kenyan Prosopis populations based on random ...

    African Journals Online (AJOL)

    To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference to Prosopis chilensis, Prosopis juliflora and Prosopis pallida using random amplified polymorphic DNA markers.

  6. RAPD analysis for genetic diversity of two populations of Mystus ...

    African Journals Online (AJOL)

    ) was applied to analyze the genetic variation of the 2 populations of Mystus vittatus (Bloch) of Madhya Pradesh, India. 10 random 10-mer primers were primarily scored in 3 individuals from each of the 2 locations. Five primers, which gave ...

  7. Genetic diversity in two populations of Limicolaria aurora (Jay, 1839 ...

    African Journals Online (AJOL)

    Limicolaria aurora belongs to the group of land snails commonly called garden snails. This study seeks to use shell morphology and random amplified polymorphic DNA-polymerase chain reaction (RAPDPCR) to examine gross morphological differences in populations of L. aurora from New Bussa (guinea savannah) and ...

  8. Allozyme diversity of selected and natural loblolly pine populations

    Science.gov (United States)

    Ronald C. Schmidtling; E. Carroll; T. LaFarge

    1999-01-01

    Loblolly pine (Pinus taeda L.) megagametophytes and embryos were examined electrophoretically to compare the extent and distribution of genetic variability in allozymes of selected and wild populations. Range-wide collections of three different types were investigated in this study. These consisted of seed sampled from (1) a provenance test...

  9. Integrating common and rare genetic variation in diverse human populations.

    Science.gov (United States)

    Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Altshuler, David M; Gibbs, Richard A; Peltonen, Leena; Dermitzakis, Emmanouil; Schaffner, Stephen F; Yu, Fuli; Peltonen, Leena; Dermitzakis, Emmanouil; Bonnen, Penelope E; Altshuler, David M; Gibbs, Richard A; de Bakker, Paul I W; Deloukas, Panos; Gabriel, Stacey B; Gwilliam, Rhian; Hunt, Sarah; Inouye, Michael; Jia, Xiaoming; Palotie, Aarno; Parkin, Melissa; Whittaker, Pamela; Yu, Fuli; Chang, Kyle; Hawes, Alicia; Lewis, Lora R; Ren, Yanru; Wheeler, David; Gibbs, Richard A; Muzny, Donna Marie; Barnes, Chris; Darvishi, Katayoon; Hurles, Matthew; Korn, Joshua M; Kristiansson, Kati; Lee, Charles; McCarrol, Steven A; Nemesh, James; Dermitzakis, Emmanouil; Keinan, Alon; Montgomery, Stephen B; Pollack, Samuela; Price, Alkes L; Soranzo, Nicole; Bonnen, Penelope E; Gibbs, Richard A; Gonzaga-Jauregui, Claudia; Keinan, Alon; Price, Alkes L; Yu, Fuli; Anttila, Verneri; Brodeur, Wendy; Daly, Mark J; Leslie, Stephen; McVean, Gil; Moutsianas, Loukas; Nguyen, Huy; Schaffner, Stephen F; Zhang, Qingrun; Ghori, Mohammed J R; McGinnis, Ralph; McLaren, William; Pollack, Samuela; Price, Alkes L; Schaffner, Stephen F; Takeuchi, Fumihiko; Grossman, Sharon R; Shlyakhter, Ilya; Hostetter, Elizabeth B; Sabeti, Pardis C; Adebamowo, Clement A; Foster, Morris W; Gordon, Deborah R; Licinio, Julio; Manca, Maria Cristina; Marshall, Patricia A; Matsuda, Ichiro; Ngare, Duncan; Wang, Vivian Ota; Reddy, Deepa; Rotimi, Charles N; Royal, Charmaine D; Sharp, Richard R; Zeng, Changqing; Brooks, Lisa D; McEwen, Jean E

    2010-09-02

    Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called 'HapMap 3', includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

  10. Directional dominance on stature and cognition in diverse human populations

    NARCIS (Netherlands)

    P.K. Joshi (Peter); T. Esko (Tõnu); H. Mattsson (Hannele); N. Eklund (Niina); I. Gandin (Ilaria); T. Nutile; A.U. Jackson (Anne); C. Schurmann (Claudia); G.D. Smith; W. Zhang (Weihua); Y. Okada (Yukinori); A. Stancáková (Alena); J.D. Faul (Jessica D.); W. Zhao (Wei); T.M. Bartz (Traci M.); M.P. Concas (Maria Pina); N. Franceschini (Nora); S. Enroth (Stefan); V. Vitart (Veronique); S. Trompet (Stella); X. Guo (Xiuqing); D.I. Chasman (Daniel); J.R. O'Connel (Jeffrey R.); T. Corre (Tanguy); S.S. Nongmaithem (Suraj S.); Y. Chen (Yuning); M. Mangino (Massimo); D. Ruggiero; M. Traglia (Michela); A.-E. Farmaki (Aliki-Eleni); T. Kacprowski (Tim); A. Bjonnes (Andrew); A. van der Spek (Ashley); Y. Wu (Ying); A.K. Giri (Anil K.); L.R. Yanek (Lisa); L. Wang (Lihua); E. Hofer (Edith); C.A. Rietveld (Niels); O. McLeod (Olga); M. Cornelis (Marilyn); C. Pattaro (Cristian); N. Verweij (Niek); C. Baumbach (Clemens); A. Abdellaoui (Abdel); H. Warren (Helen); D. Vuckovic (Dragana); H. Mei (Hao); C. Bouchard (Claude); J.R.B. Perry (John); S. Cappellani (Stefania); S.S. Mirza (Saira); M.C. Benton (Miles C.); U. Broeckel (Ulrich); S.E. Medland (Sarah Elizabeth); P.A. Lind (Penelope); G. Malerba (Giovanni); A. Drong (Alexander); L. Yengo (Loic); L.F. Bielak (Lawrence F.); D. Zhi (Degui); P.J. van der Most (Peter); D. Shriner (Daniel); R. Mägi (Reedik); G. Hemani; T. Karaderi (Tugce); Z. Wang (Zhaoming); T. Liu (Tian); I. Demuth (Ilja); J.H. Zhao (Jing Hua); W. Meng (Weihua); L. Lataniotis (Lazaros); S.W. Van Der Laan (Sander W.); J.P. Bradfield (Jonathan); A.R. Wood (Andrew); A. Bonnefond (Amélie); T.S. Ahluwalia (Tarunveer Singh); L.M. Hall (Leanne M.); E. Salvi (Erika); S. Yazar (Seyhan); L. Carstensen (Lisbeth); H.G. De Haan (Hugoline G.); M. Abney (Mark); U. Afzal (Uzma); M.A. Allison (Matthew); N. Amin (Najaf); F.W. Asselbergs (Folkert W.); S.J.L. Bakker (Stephan); R.G. Barr (Graham); S.E. Baumeister (Sebastian); D.J. Benjamin (Daniel J.); S. Bergmann (Sven); E.A. Boerwinkle (Eric); E.P. Bottinger (Erwin P.); A. Campbell (Archie); A. Chakravarti (Aravinda); Y. Chan (Yingleong); S.J. Chanock (Stephen); C. Chen (Constance); Y.-D.I. Chen (Y.-D. Ida); F.S. Collins (Francis); J. Connell (John); A. Correa (Adolfo); L.A. Cupples (Adrienne); G.D. Smith; G. Davies (Gail); M. Dörr (Marcus); G.B. Ehret (Georg); S.B. Ellis (Stephen B.); B. Feenstra (Bjarke); M.F. Feitosa (Mary Furlan); I. Ford; C.S. Fox (Caroline); T.M. Frayling (Timothy); N. Friedrich (Nele); F. Geller (Frank); G. Scotland (Generation); I. Gillham-Nasenya (Irina); R.F. Gottesman (Rebecca); M.J. Graff (Maud J.L.); F. Grodstein (Francine); C. Gu (Charles); C. Haley (Chris); C.J. Hammond (Christopher); S.E. Harris (Sarah); T.B. Harris (Tamara); N. Hastie (Nick); N.L. Heard-Costa (Nancy); K. Heikkilä (Kauko); L.J. Hocking (Lynne); G. Homuth (Georg); J.J. Hottenga (Jouke Jan); J. Huang (Jian); J.E. Huffman (Jennifer); P.G. Hysi (Pirro); M.A. Ikram (Arfan); E. Ingelsson (Erik); A. Joensuu (Anni); A. Johansson (Åsa); P. Jousilahti (Pekka); J.W. Jukema (Jan Wouter); M. Kähönen (Mika); Y. Kamatani (Yoichiro); S. Kanoni (Stavroula); S.M. Kerr (Shona); N.M. Khan (Nazir M.); Ph.D. Koellinger (Philipp); H.A. Koistinen (Heikki A.); M.K. Kooner (Manraj K.); M. Kubo (Michiaki); J. Kuusisto (Johanna); J. Lahti (Jari); L.J. Launer (Lenore); R.A. Lea (Rodney A.); B. Lehne (Benjamin); T. Lehtimäki (Terho); D.C. Liewald (David C.); L. Lind (Lars); M. Loh (Marie); M.L. Lokki; S.J. London (Stephanie J.); S.J. Loomis (Stephanie J.); A. Loukola (Anu); Y. Lu (Yingchang); T. Lumley (Thomas); A. Lundqvist (Annamari); S. Männistö (Satu); P. Marques-Vidal (Pedro); C. Masciullo (Corrado); A. Matchan (Angela); J. Mathias (Jasmine); K. Matsuda (Koichi); J.B. Meigs (James); C. Meisinger (Christa); T. Meitinger (Thomas); C. Menni (Cristina); F.D. Mentch (Frank); E. Mihailov (Evelin); L. Milani (Lili); M.E. Montasser (May E.); G.W. Montgomery (Grant); A.C. Morrison (Alanna); R.H. Myers (Richard); R. Nadukuru (Rajiv); P. Navarro (Pau); M. Nalis (Mari); M.S. Nieminen (Markku S.); I.M. Nolte (Ilja M.); G.T. O'Connor (George); A. Ogunniyi (Adesola); S. Padmanabhan (Sandosh); W. Palmas (Walter); J.S. Pankow (James); I. Patarcic (Inga); F. Pavani (Francesca); P.A. Peyser (Patricia A.); K.H. Pietilainen (Kirsi Hannele); N.R. Poulter (Neil); I. Prokopenko (Inga); S. Ralhan (Sarju); P. Redmond (Paul); S.S. Rich (Stephen S.); H. Rissanen (Harri); A. Robino (Antonietta); L.M. Rose (Lynda M.); R.J. Rose (Richard J.); C. Sala (Cinzia); B. Salako (Babatunde); V. Salomaa (Veikko); A.-P. Sarin; R. Saxena (Richa); R. Schmidt (Reinhold); L.J. Scott (Laura); W.R. Scott (William R.); B. Sennblad (Bengt); S. Seshadri (Sudha); P. Sever (Peter); S. Shrestha (Smeeta); B.H. Smith (Blair); J.A. Smith (Jennifer A); N. Soranzo (Nicole); N. Sotoodehnia (Nona); L. Southam (Lorraine); A. Stanton (Alice); M.G. Stathopoulou (Maria G); K. Strauch (Konstantin); R.J. Strawbridge (Rona); M.J. Suderman (Matthew J.); N. Tandon (Nikhil); S.-T. Tang (Sian-Tsun); K.D. Taylor (Kent D.); B. Tayo (Bamidele); A.M. Töglhofer (Anna Maria); M. Tomaszewski (Maciej); N. Tsernikova (Natalia); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); D. Vaidya (Dhananjay); A. van Hylckama Vlieg (Astrid); J. van Setten (Jessica); T. Vasankari (Tuula); S. Vedantam (Sailaja); E. Vlachopoulou (Efthymia); D. Vozzi (Diego); E. Vuoksimaa (Eero); M. Waldenberger (Melanie); E.B. Ware (Erin B.); W. Wentworth-Shields (William); J. Whitfield (John); S. Wild (Sarah); G.A.H.M. Willemsen (Gonneke); C.S. Yajnik (Chittaranjan S.); J. Yao (Jie); G. Zaza (Gianluigi); X. Zhu (Xiaofeng); R.M. Salem (Rany); M. Melbye (Mads); H. Bisgaard (Hans); N.J. Samani (Nilesh); D. Cusi (Daniele); D.A. Mackey (David A.); R.S. Cooper (Richard S.); P. Froguel (Philippe); G. Pasterkamp (Gerard); S.F.A. Grant (Struan F.A.); H. Hakonarson (Hakon); L. Ferrucci (Luigi); R.A. Scott (Robert); A.D. Morris (Andrew); C.N.A. Palmer (Colin); G.V. Dedoussis (George V.); P. Deloukas (Panagiotis); L. Bertram (Lars); U. Lindenberger (Ulman); S.I. Berndt (Sonja); C.M. Lindgren (Cecilia); N.J. Timpson (Nicholas); A. Tönjes (Anke); P. Munroe (Patricia); T.I.A. Sørensen (Thorkild I.A.); C. Rotimi (Charles); D.K. Arnett (Donna); A.J. Oldehinkel (Albertine); S.L.R. Kardia (Sharon); B. Balkau (Beverley); G. Gambaro (Giovanni); A.P. Morris (Andrew); J.G. Eriksson (Johan G.); M.J. Wright (Margaret); N.G. Martin (Nicholas); S.C. Hunt (Steven); J.M. Starr (John); I.J. Deary (Ian J.); L.R. Griffiths (Lyn R.); H.W. Tiemeier (Henning); N. Pirastu (Nicola); J. Kaprio (Jaakko); N.J. Wareham (Nick); L. Perusse (Louis); J.G. Wilson (James); S. Girotto; M. Caulfield (Mark); O.T. Raitakari (Olli T.); D.I. Boomsma (Dorret); C. Gieger (Christian); P. van der Harst; A.A. Hicks (Andrew); P. Kraft (Peter); J. Sinisalo (Juha); P. Knekt; M. Johannesson (Magnus); P.K.E. Magnusson (Patrik K. E.); A. Hamsten (Anders); R. Schmidt (Reinhold); I.B. Borecki (Ingrid); E. Vartiainen (Erkki); D.M. Becker (Diane); D. Bharadwaj (Dwaipayan); K.L. Mohlke (Karen); M. Boehnke (Michael); C.M. van Duijn (Cornelia); D.K. Sanghera (Dharambir); A. Teumer (Alexander); E. Zeggini (Eleftheria); A. Metspalu (Andres); P. Gasparini (Paolo); S. Ulivi (Shelia); C. Ober (Carole); D. Toniolo (Daniela); I. Rudan (Igor); D.J. Porteous (David J.); M. Ciullo; T.D. Spector (Timothy); C. Hayward (Caroline); J. Dupuis (Josée); R.J.F. Loos (Ruth); A. Wright (Alan); G.R. Chandak (Giriraj); P. Vollenweider (Peter); A.R. Shuldiner (Alan); P.M. Ridker (Paul); J.I. Rotter (Jerome I.); N. Sattar (Naveed); U. Gyllensten (Ulf); K.E. North (Kari); M. Pirastu (Mario); B.M. Psaty (Bruce); D.R. Weir (David); M. Laakso (Markku); V. Gudnason (Vilmundur); A. Takahashi (Atsushi); J.C. Chambers (John C.); J.S. Kooner (Jaspal S.); D.P. Strachan (David P.); H. Campbell (Harry); J.N. Hirschhorn (Joel N.); M. Perola (Markus); O. Polasek (Ozren); J.F. Wilson (James)

    2015-01-01

    textabstractHomozygosity has long been associated with rare, often devastating, Mendelian disorders, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness. However, the effect of the more distant parental relatedness that is common in modern human populations is

  11. Genetic diversity of Jatropha curcas L. populations in Kenya using ...

    African Journals Online (AJOL)

    Jatropha curcas L is an economically potential tree species gaining interest globally because of its feasible contribution towards production of commercial biofuel. Little is known however, of its genetic variation patterns within Kenyan accessions for maximum exploitation. Eight populations covering most of its distribution ...

  12. Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of Natural Calophyllum brasiliense (Clusiaceae Populations in Riparian Forests

    Directory of Open Access Journals (Sweden)

    Evânia Galvão Mendonça

    2014-01-01

    Full Text Available The objective of this study was to assess the genetic variability in two natural populations of Calophyllum brasiliense located along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958. The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001 in Rio das Mortes and 0.040 (P<0.001 in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

  13. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    Directory of Open Access Journals (Sweden)

    Yan Zheng

    Full Text Available The oriental fruit moth Grapholita ( = Cydia molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

  14. Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.

    Science.gov (United States)

    Props, Ruben; Schmidt, Marian L; Heyse, Jasmine; Vanderploeg, Henry A; Boon, Nico; Denef, Vincent J

    2018-02-01

    Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Genetic diversity of the Ethiopian Grevy's zebra (Equus grevyi) populations that includes a unique population of the Alledeghi Plain.

    Science.gov (United States)

    Kebede, Fanuel; Rosenbom, Sonia; Khalatbari, Leili; Moehlman, Patricia D; Beja-Pereira, Albano; Bekele, Afework

    2016-01-01

    The endangered Grevy's Zebra (Equus grevyi) is confined to the Horn of Africa, specifically Ethiopia and Kenya. It is threatened by habitat loss and fragmentation due to human encroachment of historic range. Knowledge of population genetics is essential for the development of appropriate conservation actions and management. The focus of this study was to assess the heterogeneity and genetic distinctiveness of the two Grevy's zebra populations in Ethiopia. Non-invasive fecal samples (N = 120) were collected during 2009-2010 from Grevy's zebra populations in the Alledeghi Wildlife Reserve and the Sarite area, Ethiopia. Analyses of a 329 bp of the mtDNA control region of 47 sequences, revealed the existence of two unreported haplotypes in the northern population of Alledeghi, that were not shared with the southern population of Sarite. The Sarite population is contiguous with the Grevy's zebra population in Kenya. The nucleotide diversity levels found in both the populations are extremely low.

  16. Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

    Science.gov (United States)

    Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

    2017-06-01

    Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

  17. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture.

    Directory of Open Access Journals (Sweden)

    John E Pool

    Full Text Available Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia, while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa F(ST were found to be enriched in genomic regions of locally

  18. Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

    Science.gov (United States)

    Pool, John E.; Corbett-Detig, Russell B.; Sugino, Ryuichi P.; Stevens, Kristian A.; Cardeno, Charis M.; Crepeau, Marc W.; Duchen, Pablo; Emerson, J. J.; Saelao, Perot; Begun, David J.; Langley, Charles H.

    2012-01-01

    Drosophila melanogaster has played a pivotal role in the development of modern population genetics. However, many basic questions regarding the demographic and adaptive history of this species remain unresolved. We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection within an African population, between African populations, and between European and African populations. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan

  19. Diversity and significance of eriophyoid mites (Acari: Eriophyoidea associated with coniferous trees in Poland: a review

    Directory of Open Access Journals (Sweden)

    Kiedrowicz Agnieszka

    2016-06-01

    Full Text Available Among the approximately 200 eriophyoid mite species associated with coniferous trees worldwide, 33 species (of the families Eriophyidae and Phytoptidae infest conifers in Poland, and 24 of them can cause visible feeding symptoms. In this paper we discuss the importance of eriophyoid mites to coniferous plants in Poland and their potential impact on the decorative value of ornamental plants. We emphasize the general lack of knowledge about the diversity of eriophyoid mites associated with coniferous trees and its role in the management and control of this economically important mite group.

  20. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    Science.gov (United States)

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

  1. Diversity of human small intestinal Streptococcus and Veillonella populations.

    Science.gov (United States)

    van den Bogert, Bartholomeus; Erkus, Oylum; Boekhorst, Jos; de Goffau, Marcus; Smid, Eddy J; Zoetendal, Erwin G; Kleerebezem, Michiel

    2013-08-01

    Molecular and cultivation approaches were employed to study the phylogenetic richness and temporal dynamics of Streptococcus and Veillonella populations in the small intestine. Microbial profiling of human small intestinal samples collected from four ileostomy subjects at four time points displayed abundant populations of Streptococcus spp. most affiliated with S. salivarius, S. thermophilus, and S. parasanguinis, as well as Veillonella spp. affiliated with V. atypica, V. parvula, V. dispar, and V. rogosae. Relative abundances varied per subject and time of sampling. Streptococcus and Veillonella isolates were cultured using selective media from ileostoma effluent samples collected at two time points from a single subject. The richness of the Streptococcus and Veillonella isolates was assessed at species and strain level by 16S rRNA gene sequencing and genetic fingerprinting, respectively. A total of 160 Streptococcus and 37 Veillonella isolates were obtained. Genetic fingerprinting differentiated seven Streptococcus lineages from ileostoma effluent, illustrating the strain richness within this ecosystem. The Veillonella isolates were represented by a single phylotype. Our study demonstrated that the small intestinal Streptococcus populations displayed considerable changes over time at the genetic lineage level because only representative strains of a single Streptococcus lineage could be cultivated from ileostoma effluent at both time points. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  2. Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE study.

    Directory of Open Access Journals (Sweden)

    Logan Dumitrescu

    2011-06-01

    Full Text Available For the past five years, genome-wide association studies (GWAS have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C, low-density lipoprotein cholesterol (LDL-C, and triglyceride (TG levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG levels in self-identified European American (~20,000, African American (~9,000, American Indian (~6,000, Mexican American/Hispanic (~2,500, Japanese/East Asian (~690, and Pacific Islander/Native Hawaiian (~175 adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92% SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05 and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG in European Americans generalized to African Americans (48%, 61%, and 57%, American Indians (45%, 64%, and 77%, and Mexican Americans/Hispanics (57%, 56%, and 86%. Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.

  3. Genetic diversity and population structure of Miscanthus sinensis germplasm in China.

    Directory of Open Access Journals (Sweden)

    Hua Zhao

    Full Text Available Miscanthus is a perennial rhizomatous C4 grass native to East Asia. Endowed with great biomass yield, high ligno-cellulose composition, efficient use of radiation, nutrient and water, as well as tolerance to stress, Miscanthus has great potential as an excellent bioenergy crop. Despite of the high potential for biomass production of the allotriploid hybrid M. ×giganteus, derived from M. sacchariflorus and M. sinensis, other options need to be explored to improve the narrow genetic base of M. ×giganteus, and also to exploit other Miscanthus species, including M. sinensis (2n = 2x = 38, as bioenergy crops. In the present study, a large number of 459 M. sinensis accessions, collected from the wide geographical distribution regions in China, were genotyped using 23 SSR markers transferable from Brachypodium distachyon. Genetic diversity and population structure were assessed. High genetic diversity and differentiation of the germplasm were observed, with 115 alleles in total, a polymorphic rate of 0.77, Nei's genetic diversity index (He of 0.32 and polymorphism information content (PIC of 0.26. Clustering of germplasm accessions was primarily in agreement with the natural geographic distribution. AMOVA and genetic distance analyses confirmed the genetic differentiation in the M. sinensis germplasm and it was grouped into five clusters or subpopulations. Significant genetic variation among subpopulations indicated obvious genetic differentiation in the collections, but within-subpopulation variation (83% was substantially greater than the between-subpopulation variation (17%. Considerable phenotypic variation was observed for multiple traits among 300 M. sinensis accessions. Nine SSR markers were found to be associated with heading date and biomass yield. The diverse Chinese M. sinensis germplasm and newly identified SSR markers were proved to be valuable for breeding Miscanthus varieties with desired bioenergy traits.

  4. Genetic diversity of Plasmodium falciparum populations in southeast and western Myanmar.

    Science.gov (United States)

    Soe, Than Naing; Wu, Yanrui; Tun, Myo Win; Xu, Xin; Hu, Yue; Ruan, Yonghua; Win, Aung Ye Naung; Nyunt, Myat Htut; Mon, Nan Cho Nwe; Han, Kay Thwe; Aye, Khin Myo; Morris, James; Su, Pincan; Yang, Zhaoqing; Kyaw, Myat Phone; Cui, Liwang

    2017-07-04

    The genetic diversity of malaria parasites reflects the complexity and size of the parasite populations. This study was designed to explore the genetic diversity of Plasmodium falciparum populations collected from two southeastern areas (Shwekyin and Myawaddy bordering Thailand) and one western area (Kyauktaw bordering Bangladesh) of Myanmar. A total of 267 blood samples collected from patients with acute P. falciparum infections during 2009 and 2010 were used for genotyping at the merozoite surface protein 1 (Msp1), Msp2 and glutamate-rich protein (Glurp) loci. One hundred and eighty four samples were successfully genotyped at three genes. The allelic distributions of the three genes were all significantly different among three areas. MAD20 and 3D7 were the most prevalent alleles in three areas for Msp1 and Msp2, respectively. The Glurp allele with a bin size of 700-750 bp was the most prevalent both in Shwekyin and Myawaddy, whereas two alleles with bin sizes of 800-850 bp and 900-1000 bp were the most prevalent in the western site Kyauktaw. Overall, 73.91% of samples contained multiclonal infections, resulting in a mean multiplicity of infection (MOI) of 1.94. Interestingly, the MOI level presented a rising trend with the order of Myawaddy, Kyauktaw and Shwekyin, which also paralleled with the increasing frequencies of Msp1 RO33 and Msp2 FC27 200-250 bp alleles. Msp1 and Msp2 genes displayed higher levels of diversity and higher MOI rates than Glurp. PCR revealed four samples (two from Shwekyin and two from Myawaddy) with mixed infections of P. falciparum and P. vivax. This study genotyped parasite clinical samples from two southeast regions and one western state of Myanmar at the Msp1, Msp2 and Glurp loci, which revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations at these sites. The results indicated that malaria transmission intensity in these regions remained high and more strengthened control efforts are

  5. Social Support Networks Among Diverse Sexual Minority Populations

    Science.gov (United States)

    Frost, David M.; Meyer, Ilan H.; Schwartz, Sharon

    2016-01-01

    This paper reports a study of the function and composition of social support networks among diverse lesbian, gay and bisexual (LGB) men and women (n = 396) in comparison to their heterosexual peers (n = 128). Data were collected using a structured social support network matrix in a community sample recruited in New York City. Our findings show that gay and bisexual men may rely on “chosen families” within LGBT communities more so than lesbian and bisexual women. Both heterosexuals and LGBs relied less on family and more on other people (e.g., friends, co-workers) for everyday social support (e.g., recreational and social activities, talking about problems). Providers of everyday social support were most often of the same sexual orientation and race/ethnicity as participants. In seeking major support (e.g., borrowing large sums of money), heterosexual men and women along with lesbian and bisexual women relied primarily on their families, but gay and bisexual men relied primarily on other LGB individuals. Racial/ethnic minority LGBs relied on LGB similar others at the same rate at White LGBs but, notably, racial/ethnic minority LGBs reported receiving fewer dimensions of support. PMID:26752447

  6. Communication Adaptations for a Diverse International Patient Population.

    Science.gov (United States)

    Ghosh, Aditya; Joshi, Shashank; Ghosh, Amit K

    2017-11-01

    We live in an age of hyper connectivity, people from around the world are looking outside their own national borders to receive medical care. As more people are learning about the quality that the elite Indian hospitals provide at a competitive, and often more affordable, price compared to other institutions around the world, they are becoming increasingly interested in receiving their medical care in Indian hospitals. It is for this exact reason that it is very important to learn the importance of communicating effectively with people from a diverse background. Over the next decade, the number of international patients that Indian hospitals will provide care for is set to dramatically increase. In this new age of medicine in India, it is imperative that doctors are adequately equipped with the communication skills to appropriately connect with patients coming from very different cultural backgrounds. The interaction with an international patient can be tremendously deepened through effective communication that adheres to the cultural beliefs of the patient. In this article, we detail how to effectively communicate with people from different backgrounds. We explore how to speak with patients and connect on a deeper level and respect the cultural differences that exist. We will also discuss how to avoid offending your patients or miscommunicating your plans to them. Overall, improved awareness of cultural differences will ensure higher patient satisfaction as well as an improved doctor patient interaction. © Journal of the Association of Physicians of India 2011.

  7. Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.

    Science.gov (United States)

    Santos, Eduarda M; Hamilton, Patrick B; Coe, Tobias S; Ball, Jonathan S; Cook, Alastair C; Katsiadaki, Ioanna; Tyler, Charles R

    2013-10-15

    Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Low Genetic Diversity and Structuring of the Arapaima (Osteoglossiformes, Arapaimidae Population of the Araguaia-Tocantins Basin

    Directory of Open Access Journals (Sweden)

    Carla A. Vitorino

    2017-10-01

    Full Text Available The arapaima, Arapaima gigas, is a fish whose populations are threatened by both overfishing and the ongoing destruction of its natural habitats. In the Amazon basin, varying levels of population structure have been found in A. gigas, although no data are available on the genetic diversity or structure of the populations found in the Araguaia-Tocantins basin, which has a topographic profile, hydrological regime, and history of fishing quite distinct from those of the Amazon. In this context, microsatellite markers were used to assess the genetic diversity and connectivity of five wild A. gigas populations in the Araguaia-Tocantins basin. The results of the analysis indicated low levels of genetic diversity in comparison with other A. gigas populations, studied in the Amazon basin. The AMOVA revealed that the Arapaima populations of the Araguaia-Tocantins basin are structured significantly. No correlation was found between pairwise FST values and the geographical distance among populations. The low level of genetic variability and the evidence of restricted gene flow may both be accounted for by overfishing, as well as the other human impacts that these populations have been exposed to over the years. The genetic fragility of these populations demands attention, given that future environmental changes (natural or otherwise may further reduce these indices and eventually endanger these populations. The results of this study emphasize the need to take the genetic differences among the study populations into account when planning management measures and conservation strategies for the arapaima stocks of the Araguaia-Tocantins basin.

  9. Genetic diversity of macauba from natural populations of Brazil.

    Science.gov (United States)

    da Conceição, Léo Duc Haa Carson Schwartzhaupt; Antoniassi, Rosemar; Junqueira, Nilton Tadeu Vilela; Braga, Marcelo Fideles; de Faria-Machado, Adelia Ferreira; Rogério, Joice Barbosa; Duarte, Iara Duprat; Bizzo, Humberto Ribeiro

    2015-09-04

    The macauba has been identified as the most promising native species for the production of vegetable oil and biomass. Several studies confirm its potential for numerous purposes (liquid and solid biofuels, food, cosmetics and pharmaceuticals), but this Brazilian biodiversity resource has been little explored, and work aimed at their domestication and genetic improvement are relatively recent. This study consisted of a multivariate approach to levels of trans fatty acids, oil yield and physical characteristics found in fruits of macauba of natural populations. The objective was to quantify the genetic variability among 35 genotypes of natural populations of macauba from 16 locations in different regions of Brazil. Euclidean Distance measurements were estimated and the cluster analysis obtained by the UPGMA method considering separately the fatty acid profile, and traits related to physical part and the fruits oil content. It was observed the formation of seven groups for the profile of fatty acids and five groups for physical characteristics and oil yield. Large variations were observed for different types of mesocarp (pulp) fatty acids and kernel. Oleic acid (18: 1) in mesocarp was the largest contribution to the total divergence. The results indicate variations to the physical characteristics and oil yield, especially the oil percentage in mesocarp and weight of the whole fruit which contributed 64.58% of the divergence between genotypes. The study identified genotypes potential to generate variability and obtaining selection gains, directing plant breeding programs according with demands of oils market.

  10. Controlling the diversity of cell populations in a stem cell culture

    NARCIS (Netherlands)

    Heo, Inha; Clevers, Hans

    2015-01-01

    Culturing intestinal stem cells into 3D organoids results in heterogeneous cell populations, reflecting the in vivo cell type diversity. In a recent paper published in Nature, Wang et al. established a culture condition for a highly homogeneous population of intestinal stem cells.

  11. Consistent loss of genetic diversity in isolated cutthroat trout populations independent of habitat size and quality

    Science.gov (United States)

    Kellie J. Carim; Lisa A. Eby; Craig A. Barfoot; Matthew C. Boyer

    2016-01-01

    Fragmentation and isolation of wildlife populations has reduced genetic diversity worldwide, leaving many populations vulnerable to inbreeding depression and local extinction. Nonetheless, isolation is protecting many native aquatic species from interactions with invasive species, often making reconnection an unrealistic conservation strategy. Isolation management is...

  12. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  13. Genetic diversity of Dyera polyphylla (Miq.) Steenis populations used in tropical peatland restoration in Indonesia

    NARCIS (Netherlands)

    Tata, Hesti Lestari; Muchugi, A.; Kariba, R.; Noordwijk, van M.

    2018-01-01

    Dyera polyphylla is a native tree species of peat swamp forests in Southeast Asia. Where it has been used in peatland restoration, the trees are of uncertain genetic origin. We analysed the genetic diversity of seven populations of D. polyphylla (9–20 individual trees per population) from both

  14. Genetic diversity and population differentiation of small giant clam Tridacna maxima in Comoros islands assessed by microsatellite markers.

    Science.gov (United States)

    Ahmed Mohamed, Nadjim; Yu, Qian; Chanfi, Mohamed Ibrahim; Li, Yangping; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin

    2016-01-01

    Small giant clam, Tridacna maxima , widely distributed from French Polynesia to East Africa, has faced population declines due to over-exploitation. Comoros islands are an important biogeographic region due to potential richness of marine species, but no relevant information is available. In order to facilitate devising effective conservation management plan for T. maxima , nine microsatellite markers were used to survey genetic diversity and population differentiation of 72 specimens collected from three Comoros islands, Grande Comore, Moheli and Anjouan. A total of 51 alleles were detected ranged from 2 to 8 per locus. Observed and expected heterozygosity varied from 0.260 to 0.790 and from 0.542 to 0.830, respectively. All populations have high genetic diversity, especially the population in Moheli, a protected area, has higher genetic diversity than the others. Significant heterozygote deficiencies were recorded, and null alleles were probably the main factor leading to these deficits. F ST value indicated medium genetic differentiation among the populations. Although significant, AMOVA revealed 48.9 % of genetic variation within individuals and only a small variation of 8.9 % was found between populations. Gene flow was high ( Nm  = 12.40) between Grande Comore and Moheli, while lower ( Nm  = 1.80) between Grande Comore and Anjouan, explaining geographic barriers to genetic exchanges might exist in these two islands. Global gene flow analysis ( Nm  = 5.50) showed that larval dispersal is enough to move between the islands. The high genetic diversity and medium population differentiation revealed in the present study offer useful information on genetic conservation of small giant clams.

  15. RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

    Science.gov (United States)

    Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

    2017-02-08

    Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of F ST and R ST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

  16. Genetic Diversity and Population Structure of a Threatened African Tree Species, Milicia excelsa, Using Nuclear Micro satellites DNA Markers

    International Nuclear Information System (INIS)

    Ouinsavi, Ch.; Sokpon, N.; Ouinsavi, Ch.; Khasa, D.P.

    2009-01-01

    To accurately estimate the genetic diversity and population structure for improved conservation planning of Milicia excelsa tree, 212 individuals from twelve population samples covering the species' range in Benin were surveyed at seven specific micro satellite DNA loci. All loci were variable, with the mean number of alleles per locus ranging from 5.86 to 7.69. Considerable genetic variability was detected for all populations at the seven loci (AR=4.60; HE=0.811). Moderate but statistically significant genetic differentiation was found among populations considering both FST (0.112) and RST (0.342). All of the populations showed heterozygosity deficits in test of Hardy-Weinberg Equilibrium and significantly positive FIS values due to inbreeding occurring in the species. Pairwise FST values were positively and significantly correlated with geographical distances (r=0.432; P=.007, Mantel's test) indicating that populations are differentiated by isolation by distance. Bayesian analysis of population structure showed division of the genetic variation into four clusters revealing the existence of heterogeneity in population genetic structure. Altogether, these results indicate that genetic variation in Milicia excelsa is geographically structured. Information gained from this study also emphasized the need for in situ conservation of the relict populations and establishment of gene flow corridors through agroforestry systems for interconnecting these remnant populations.

  17. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  18. Investigating the Genetic Diversity, Population Differentiation and Population Dynamics of Cycas segmentifida (Cycadaceae Endemic to Southwest China by Multiple Molecular Markers

    Directory of Open Access Journals (Sweden)

    Xiuyan Feng

    2017-05-01

    Full Text Available Climate change, species dispersal ability and habitat fragmentation are major factors influencing species distribution and genetic diversity, especially for the range-restricted and threatened taxa. Here, using four sequences of chloroplast DNAs (cpDNAs, three nuclear genes (nDNAs and 12 nuclear microsatellites (SSRs, we investigated the genetic diversity, genetic structure, divergence time and population dynamics of Cycas segmentifida D. Y. Wang and C. Y. Deng, a threatened cycad species endemic to Southwest China. High levels of genetic diversity and genetic differentiation were revealed in C. segmentifida. Haplotypes of networks showed two evolutionary units in C. segmentifida, with the exception of the nuclear gene GTP network. Meanwhile, the UPGMA tree, structure and PCoA analyses suggested that 14 populations of C. segmentifida were divided into two clades. There was significant effect of isolation by distance (IBD in this species. However, this species did not display a significant phylogeographic structure. The divergence time estimation suggested that its haplotypes diverged during the Middle Pleistocene. Additionally, the population dynamics inferred from different DNA sequences analyses were discordant. Bottleneck analysis showed that populations of C. segmentifida did not experience any recent bottleneck effect, but rather pointed to a contraction of its effective population size over time. Furthermore, our results suggested that the population BM which held an intact population structure and occupied undisturbed habitat was at the Hardy–Weinberg equilibrium, implying that this population is a free-mating system. These genetic features provide important information for the sustainable management of C. segmentifida.

  19. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  20. Assessment of genetically significant doses to the Sofia population from natural gamma background

    International Nuclear Information System (INIS)

    Vasilev, G.; Khristova, M.

    1977-01-01

    Genetically significant dose to the population of Sofia city was assessed within a program covering larger urban communities in the country. Measurements were made of gamma background exposure rates in the gonadal region. Gonad doses were estimated using a screening factor of 0.73. Based on statistical data for total number of inhabitants and number of people of reproductive age, and on the mean annual gonad doses derived, calculations were made of genetically significant dose to the Sofia population. Base-line data were thus provided for an assessment of extra radiation dose resulting from occupational radiation exposure. (author)

  1. Comparisons of genetic diversity in captive versus wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr; Lepidoptera: Nymphalidae)

    Science.gov (United States)

    Miller, Mark P.; Pratt, Gordon F.; Mullins, Thomas D.; Haig, Susan M.

    2014-01-01

    Captive populations can play a significant role in threatened and endangered species management. An important consideration when developing and managing captive populations, however, is the maintenance of genetic diversity to ensure that adequate variation exists to avoid the negative consequences of inbreeding. In this investigation, we compared genetic diversity patterns within captive and wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr [Lepidoptera: Nymphalidae]), a taxon with a restricted distribution to chaparral and sage shrublands within Riverside and San Diego counties, California. Our analyses revealed that medium to high-frequency alleles from the wild populations were also present in the captive populations. While there was no significant difference in genetic diversity as quantified by expected heterozygosity, the captive populations showed tendencies toward significantly lower allelic richness than their wild counterparts. Given that alleles from the wild populations were occasionally not detected in captive populations, periodic incorporation of new wild specimens into the captive population would help ensure that allelic diversity is maintained to the extent possible. If performed in advance, genetic surveys of wild populations may provide the clearest insights regarding the number of individuals needed in captivity to adequately reflect wild populations.

  2. Genomic Diversity Using Copy Number Variations in Worldwide Chicken Populations

    Directory of Open Access Journals (Sweden)

    Erica Gorla

    2018-06-01

    Full Text Available Recently, many studies in livestock have focused on the identification of Copy Number Variants (CNVs using high-density Single Nucleotide Polymorphism (SNP arrays, but few have focused on studying chicken ecotypes coming from many locations. CNVs are polymorphisms, which may influence phenotype and are an important source of genetic variation in populations. The aim of this study was to explore the genetic difference and structure, using a high density SNP chip in 936 individuals from seven different countries (Brazil, Italy, Egypt, Mexico, Rwanda, Sri Lanka and Uganda. The DNA was genotyped with the Affymetrix Axiom®600k Chicken Genotyping Array and processed with stringent quality controls to obtain 559,201 SNPs in 915 individuals. The Log R Ratio (LRR and the B Allele Frequency of SNPs were used to perform the CNV calling with PennCNV software based on a Hidden Markov Model analysis and the LRR was used to perform CNV detection with SVS Golden Helix software.After filtering, a total of 19,027 CNVs were detected with the SVS software, while 9,065 CNVs were identified with the Penn CNV software. The CNVs were summarized in 7,001 Copy Number Variant Regions (CNVRs and 4,414 CNVRs, using the software BedTool.The consensus analysis across the CNVRs allowed the identification of 2,820 consensus CNVR, of which 1,721 were gain, 637 loss and 462 complex, for a total length of 53 Mb corresponding to the 5 % of the GalGal5 chicken autosomes. Only the consensus CNV regions obtained from both detections were considered for further analysis.The intersection analysis performed between the chicken gene database (Gallus_gallus-5.0 and the 1,927 consensus CNVRs allowed the identification (within or partial overlap of a total of 2,354 unique genes with an official gene ID.  The CNVRs identified here represent the first comprehensive mapping in several worldwide populations, using a high-density SNP chip.

  3. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

  4. Documentation of Significant Losses in Cornus florida L. Populations throughout the Appalachian Ecoregion

    International Nuclear Information System (INIS)

    Oswalt, Ch.M.; Oswalt, S.N.

    2010-01-01

    Over the last three decades the fungus Discula destructiva Redlin has severely impacted Cornus florida L. (flowering dogwood hereafter dogwood) populations throughout its range. This study estimates historical and current dogwood populations (number of trees) across the Appalachian ecoregion. Objectives were to (1) quantify current dogwood populations in the Appalachian eco region, (2) quantify change over time in dogwood populations, and (3) identify trends in dogwood population shifts. Data from the USDA Forest Service Forest Inventory and Analysis (FIA) database were compiled from 41 FIA units in 13 states for county-level estimates of the total number of all live dogwood trees on timberland within the Appalachian eco region. Analysis of covariance, comparing historical and current county-level dogwood population estimates with average change in forest density as the covariate, was used to identify significant changes within FIA units. Losses ranging from 25 to 100 percent of the sample population (ρ<.05) were observed in 33 of the 41 (80 percent) sampled FIA units. These results indicate that an important component of the eastern deciduous forest has experienced serious losses throughout the Appalachians and support localized empirical results and landscape-scale anecdotal evidence.

  5. Documentation of Significant Losses in Cornus florida L. Populations throughout the Appalachian Ecoregion

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    Christopher M. Oswalt

    2010-01-01

    Full Text Available Over the last three decades the fungus Discula destructiva Redlin has severely impacted Cornus florida L. (flowering dogwood—hereafter “dogwood” populations throughout its range. This study estimates historical and current dogwood populations (number of trees across the Appalachian ecoregion. Objectives were to (1 quantify current dogwood populations in the Appalachian ecoregion, (2 quantify change over time in dogwood populations, and (3 identify trends in dogwood population shifts. Data from the USDA Forest Service Forest Inventory and Analysis (FIA database were compiled from 41 FIA units in 13 states for county-level estimates of the total number of all live dogwood trees on timberland within the Appalachian ecoregion. Analysis of covariance, comparing historical and current county-level dogwood population estimates with average change in forest density as the covariate, was used to identify significant changes within FIA units. Losses ranging from 25 to 100 percent of the sample population (<.05 were observed in 33 of the 41 (80 percent sampled FIA units. These results indicate that an important component of the eastern deciduous forest has experienced serious losses throughout the Appalachians and support localized empirical results and landscape-scale anecdotal evidence.

  6. Study of human genetic diversity : inferences on population origin and history

    OpenAIRE

    Haber, Marc, 1980-

    2013-01-01

    Patterns of human genetic diversity suggest that all modern humans originated from a small population in Africa that expanded rapidly 50,000 years ago to occupy the whole world. While moving into new environments, genetic drift and natural selection affected populations differently, creating genetic structure. By understanding the genetic structure of human populations, we can reconstruct human history and understand the genetic basis of diseases. The work presented here contributes to the on...

  7. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-06-17

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

  8. Population diversity of ammonium oxidizers investigated by specific PCR amplification

    Science.gov (United States)

    Ward, B.B.; Voytek, M.A.; Witzel, K.-P.

    1997-01-01

    The species composition of ammonia-oxidizing bacteria in aquatic environments was investigated using PCR primers for 16S rRNA genes to amplify specific subsets of the total ammonia-oxidizer population. The specificity of the amplification reactions was determined using total genomic DNA from known nitrifying strains and non-nitrifying strains identified as having similar rDNA sequences. Specificity of amplification was determined both for direct amplification, using the nitrifier specific primers, and with nested amplification, in which the nitrifier primers were used to reamplify a fragment obtained from direct amplification with Eubacterial universal primers. The present level of specificity allows the distinction between Nitrosomonas europaea, Nitrosomonas sp. (marine) and the other known ammonia-oxidizers in the beta subclass of the Proteobacteria. Using total DNA extracted from natural samples, we used direct amplification to determine presence/absence of different species groups. Species composition was found to differ among depths in vertical profiles of lake samples and among samples and enrichments from various other aquatic environments. Nested PCR yielded several more positive reactions, which implies that nitrifier DNA was present in most samples, but often at very low levels.

  9. Genetic diversity, kinship analysis, and broodstock management of captive Atlantic sturgeon for population restoration

    Science.gov (United States)

    Henderson, A.P.; Spidle, A.P.; King, T.L.

    2005-01-01

    Captive Atlantic sturgeon Acipenser oxyrinchus considered for use as broodstock in a restoration program were genotyped using nuclear DNA microsatellites and compared to wild collections from the Hudson River, New York (source of parents of the captive sturgeon) and from Albemarle Sound, North Carolina. Because the potential broodfish were the progeny of a small number of parents, maintaining genetic diversity and minimizing inbreeding is essential to a successful breeding and supplementation program. The microsatellite loci used in this analysis generated unique multilocus genotypes for each of 136 Atlantic sturgeon. Analyses indicated significant genetic separation between the New York and North Carolina collections and correctly identified the potential broodstock as a subset of the Hudson River population. Pairwise genetic distance (-In proportion of shared alleles) between half and full siblings in the potential broodfish was as great as 1.386, a value exceeded by only 36% of the sampled broodfish pairs available for mating. Because the current broodstock population does not seem to have deviated far from their ancestral population in the Hudson River, progeny from that broodstock, or the parents themselves, would seem to be genetically suitable for release back into the Hudson River.

  10. Genetic diversity in two Japanese flounder populations from China seas inferred using microsatellite markers and COI sequences

    Science.gov (United States)

    Xu, Dongdong; Li, Sanlei; Lou, Bao; Zhang, Yurong; Zhan, Wei; Shi, Huilai

    2012-07-01

    Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data ( F st =0.048 7, P <0.001) and mitochondrial DNA data ( F st =0.128, P <0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese

  11. Genetic diversity in different populations of sloths assessed by DNA fingerprinting

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    MORAES N.

    2002-01-01

    Full Text Available In this study we analyzed a population of Bradypus torquatus with individuals originally distributed in different localities of Bahia, and two populations of B. variegatus with individuals from Bahia and São Paulo States. Using the DNA fingerprinting method, we assessed the genetic variability within and between populations. Analysis of the DNA profiles revealed genetic similarity indices ranging from 0.34 ± 0.07 to 0.87 ± 0.04. Similar low levels of genetic variability were found only in isolated mammalian populations or among related individuals. This study presents the first analyses of genetic diversity in sloth populations.

  12. Arylamine N-acetyltransferase 2 (NAT2 genetic diversity and traditional subsistence: a worldwide population survey.

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    Audrey Sabbagh

    Full Text Available Arylamine N-acetyltransferase 2 (NAT2 is involved in human physiological responses to a variety of xenobiotic compounds, including common therapeutic drugs and exogenous chemicals present in the diet and the environment. Many questions remain about the evolutionary mechanisms that have led to the high prevalence of slow acetylators in the human species. Evidence from recent surveys of NAT2 gene variation suggests that NAT2 slow-causing variants might have become targets of positive selection as a consequence of the shift in modes of subsistence and lifestyle in human populations in the last 10,000 years. We aimed to test more extensively the hypothesis that slow acetylation prevalence in humans is related to the subsistence strategy adopted by the past populations. To this end, published frequency data on the most relevant genetic variants of NAT2 were collected from 128 population samples (14,679 individuals representing different subsistence modes and dietary habits, allowing a thorough analysis at both a worldwide and continent scale. A significantly higher prevalence of the slow acetylation phenotype was observed in populations practicing farming (45.4% and herding (48.2% as compared to populations mostly relying on hunting and gathering (22.4% (P = 0.0007. This was closely mirrored by the frequency of the slow 590A variant that was found to occur at a three-fold higher frequency in food producers (25% as compared to hunter-gatherers (8%. These findings are consistent with the hypothesis that the Neolithic transition to subsistence economies based on agricultural and pastoral resources modified the selective regime affecting the NAT2 acetylation pathway. Furthermore, the vast amount of data collected enabled us to provide a comprehensive and up-to-date description of NAT2 worldwide genetic diversity, thus building up a useful resource of frequency data for further studies interested in epidemiological or anthropological research

  13. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

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    Olsen Kenneth M

    2010-06-01

    Full Text Available Abstract Background Weedy rice (red rice, a conspecific weed of cultivated rice (Oryza sativa L., is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

  14. How closely does genetic diversity in finite populations conform to predictions of neutral theory? Large deficits in regions of low recombination.

    Science.gov (United States)

    Frankham, R

    2012-03-01

    Levels of genetic diversity in finite populations are crucial in conservation and evolutionary biology. Genetic diversity is required for populations to evolve and its loss is related to inbreeding in random mating populations, and thus to reduced population fitness and increased extinction risk. Neutral theory is widely used to predict levels of genetic diversity. I review levels of genetic diversity in finite populations in relation to predictions of neutral theory. Positive associations between genetic diversity and population size, as predicted by neutral theory, are observed for microsatellites, allozymes, quantitative genetic variation and usually for mitochondrial DNA (mtDNA). However, there are frequently significant deviations from neutral theory owing to indirect selection at linked loci caused by balancing selection, selective sweeps and background selection. Substantially lower genetic diversity than predicted under neutrality was found for chromosomes with low recombination rates and high linkage disequilibrium (compared with 'normally' recombining chromosomes within species and adjusted for different copy numbers and mutation rates), including W (median 100% lower) and Y (89% lower) chromosomes, dot fourth chromosomes in Drosophila (94% lower) and mtDNA (67% lower). Further, microsatellite genetic and allelic diversity were lost at 12 and 33% faster rates than expected in populations adapting to captivity, owing to widespread selective sweeps. Overall, neither neutral theory nor most versions of the genetic draft hypothesis are compatible with all empirical results.

  15. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Science.gov (United States)

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  16. The prevalence and clinical significance of maxillary sinus mucous retention cysts in a general clinic population.

    Science.gov (United States)

    Rhodus, N L

    1990-02-01

    Previous studies have documented the occurrence and potential clinical significance of MSMR cysts. Studies also have alluded to a relationship between the MSMR cyst and certain signs or symptoms of disease. We determined the prevalence of MSMR cysts in a general clinic population and identified some important correlations with clinical signs and symptoms.

  17. Genetic diversity in India and the inference of Eurasian population expansion.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Hu, Ya; Huff, Chad D; Sabo, Aniko; Muzny, Donna M; Bamshad, Michael J; Gibbs, Richard A; Jorde, Lynn B; Yu, Fuli

    2010-01-01

    Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans. Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia. © 2010 Xing et al.; licensee BioMed Central Ltd.

  18. Genetic diversity and population structure of Prunus mira (Koehne from the Tibet plateau in China and recommended conservation strategies.

    Directory of Open Access Journals (Sweden)

    Wenquan Bao

    Full Text Available Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17 within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%, whereas morphological analyses revealed low variation (1.30%-36.17% within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units

  19. Distance from Africa, not climate, explains within-population phenotypic diversity in humans

    Science.gov (United States)

    Betti, Lia; Balloux, François; Amos, William; Hanihara, Tsunehiko; Manica, Andrea

    2008-01-01

    The relative importance of ancient demography and climate in determining worldwide patterns of human within-population phenotypic diversity is still open to debate. Several morphometric traits have been argued to be under selection by climatic factors, but it is unclear whether climate affects the global decline in morphological diversity with increasing geographical distance from sub-Saharan Africa. Using a large database of male and female skull measurements, we apply an explicit framework to quantify the relative role of climate and distance from Africa. We show that distance from sub-Saharan Africa is the sole determinant of human within-population phenotypic diversity, while climate plays no role. By selecting the most informative set of traits, it was possible to explain over half of the worldwide variation in phenotypic diversity. These results mirror those previously obtained for genetic markers and show that ‘bones and molecules’ are in perfect agreement for humans. PMID:19129123

  20. Genetic Diversity of Plasmodium falciparum Populations in Malaria Declining Areas of Sabah, East Malaysia.

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    Mohd Ridzuan Mohd Abd Razak

    Full Text Available Malaysia has a national goal to eliminate malaria by 2020. Understanding the genetic diversity of malaria parasites in residual transmission foci can provide invaluable information which may inform the intervention strategies used to reach elimination targets. This study was conducted to determine the genetic diversity level of P. falciparum isolates in malaria residual foci areas of Sabah. Malaria active case detection was conducted in Kalabakan and Kota Marudu. All individuals in the study sites were screened for malaria infection by rapid diagnostic test. Blood from P. falciparum-infected individuals were collected on filter paper prior to DNA extraction. Genotyping was performed using merozoite surface protein-1 (MSP-1, merozoite surface protein-2 (MSP-2, glutamate rich protein (GLURP and 10 neutral microsatellite loci markers. The size of alleles, multiplicity of infection (MOI, mean number of alleles (Na, expected heterozygosity (He, linkage disequilibrium (LD and genetic differentiation (FST were determined. In Kalabakan, the MSP-1 and MSP-2 alleles were predominantly K1 and FC27 family types, respectively. The GLURP genotype VI (751-800 bp was predominant. The MOI for MSP-1 and MSP-2 were 1.65 and 1.20, respectively. The Na per microsatellite locus was 1.70. The He values for MSP-1, MSP-2, GLURP and neutral microsatellites were 0.17, 0.37, 0.70 and 0.33, respectively. In Kota Marudu, the MSP-1 and MSP-2 alleles were predominantly MAD20 and 3D7 family types, respectively. The GLURP genotype IV (651-700 bp was predominant. The MOI for both MSP-1 and MSP-2 was 1.05. The Na per microsatellite locus was 3.60. The He values for MSP-1, MSP-2, GLURP and neutral microsatellites were 0.24, 0.25, 0.69 and 0.30, respectively. A significant LD was observed in Kalabakan (0.495, p<0.01 and Kota Marudu P. falciparum populations (0.601, p<0.01. High genetic differentiation between Kalabakan and Kota Marudu P. falciparum populations was observed (FST = 0

  1. Diversity

    Science.gov (United States)

    Portraits In Courage Vol. VIII Portraits In Courage Vol. IX Portraits In Courage Vol. X AF Sites Social -Wide Initiative to Promote Diversity and Inclusion in the Federal Workforce Executive Order 13548 : Virtual Diversity Conference Air Force Diversity & Inclusion Air Force Diversity Graphic There is no

  2. The significance and role of local self-governments in the population policy of Serbia

    Directory of Open Access Journals (Sweden)

    Gavrilović Ana

    2011-01-01

    Full Text Available Population should be in the central focus of local community institutions and the local community may constitute its population policy which will supplement state population policy measures, considering the local specific various traditions, values and models of living. The paper's basic goal is to critically perceive the characteristics, significance and role of local self-governments in the current population policy of Serbia. Social situation and social policy characteristics in Serbia are analyzed in the context of the population policy. It is pointed out that poverty, unemployment, the economic crisis, the process of privatization, the issue of system decentralization and social expectations of the population, as current expressions of transition, all have a consequence on the demographic development and population policy. A critical estimation of the activities in the field of population policies which are carried out by local and provincial self-governments in Serbia in the last decade are brought into focus, with a special review to the activities of provincial and local governments in the Autonomous Province of Vojvodina. As a result of the analysis it is pointed out that the population and social policy measures have been separated since the year 2000 and that they have been directed only to stimulating births and not child raising and that solutions regarding maternity leave brought improvements, however shortened maternity leave for the third child. The new conception of the population policy brought a whole series of restrictions such as: suspension of aid for newborn essentials; discontinuance of the right to maternity allowance; abolishing of compensation for preschool expenses for the third child; children’s allowance lost its population measures character along with considerable tightening of the census and decreasing of amount; the activities of preschool facilities have been reduced only to an educational function, and the

  3. Diversity and population characteristics of terrestrial isopods (Crustacea, Oniscidea across three forest environments in southern Brazil

    Directory of Open Access Journals (Sweden)

    Priscila da Silva Bugs

    2014-09-01

    Full Text Available Terrestrial isopods are important and dominant component of meso and macrodecomposer soil communities. The present study investigates the diversity and species composition of terrestrial isopods on three forests on the Serra Geral of the state of Rio Grande do Sul, Brazil. The area has two natural formations (Primary Woodland and Secondary Woodland and one plantation of introduced Pinus. The pitfall traps operated from March 2001 to May 2002, with two summer periods and one winter. There were 14 sampling dates overall. Of the five species found: Alboscia silveirensis Araujo, 1999, Atlantoscia floridana (van Name, 1940, Benthana araucariana Araujo & Lopes, 2003 (Philoscidae, Balloniscus glaber Araujo & Zardo, 1995 (Balloniscidae and Styloniscus otakensis (Chilton, 1901 (Styloniscidae; only A. floridana is abundant on all environments and B. glaber is nearly exclusive for the native forests. The obtained data made it possible to infer about population characteristics of this species. The Similarity Analysis showed a quantitative difference among the Secondary forest and Pinus plantation, but not a qualitative one. The operational sex ratio (OSR analysis for A. floridana does not reveal significant differences in male and female proportions among environments. The reproductive period identified in the present study for A. floridana was from spring to autumn in the primary forest and Pinus plantation and during all year for the secondary forest. The OSR analysis for B. glaber reveals no significant differences in abundance between males and females for secondary forest, but the primary forest was a significant difference. The reproductive period for B. glaber extended from summer to autumn (for primary and secondary forest. This is the first record for Brazil of an established terrestrial isopod population in a Pinus sp. plantation area, evidenced by the presence of young, adults and ovigerous females, balanced sex ratio, expected fecundity and

  4. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

    Science.gov (United States)

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-01-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

  5. Genetic structure and diversity in Juniperus communis populations in Saxony, Germany

    Directory of Open Access Journals (Sweden)

    Reim Stefanie

    2016-06-01

    Full Text Available In recent years, land use changes led to a rapid decline and fragmentation of J. communis populations in Germany. Population isolation may lead to a restricted gene flow and, further, to negative effects on genetic variation. In this study, genetic diversity and population structure in seven fragmented J. communis populations in Saxony, Germany, were investigated using nuclear microsatellites (nSSR and chloroplast single nucleotide polymorphism (cpSNP. In all Saxony J. communis populations, a high genetic diversity was determined but no population differentiation could be detected whatever method was applied (Bayesian cluster analysis, F-statistics, AMOVA. The same was true for three J. communis out-group samples originating from Italy, Slovakia and Norway, which also showed high genetic diversity and low genetic differences regarding other J. communis populations. Low genetic differentiation among the J. communis populations ascertained with nuclear and chloroplast markers indicated high levels of gene flow by pollen and also by seeds between the sampled locations. Low genetic differentiation may also provide an indicator of Juniper survival during the last glacial maximum (LGM in Europe. The results of this study serve as a basis for the implementation of appropriate conservation measures in Saxony.

  6. Genetic Diversity in Jatropha curcas Populations in the State of Chiapas, Mexico

    Directory of Open Access Journals (Sweden)

    Miguel Salvador-Figueroa

    2011-10-01

    Full Text Available Jatropha curcas L. has become an important source of oil production for biodiesel fuel. Most genetic studies of this plant have been conducted with Asian and African accessions, where low diversity was encountered. There are no studies of this kind focusing in the postulated region of origin. Therefore, five populations of J. curcas were studied in the state of Chiapas, Mexico, using amplified fragment length polymorphism (AFLP markers. One hundred and fifty-two useful markers were obtained: overall polymorphism = 81.18% and overall Nei’s genetic diversity (He = 0.192. The most diverse population was the Border population [He: 0.245, Shanon’s information index (I: 0.378]. A cluster analysis revealed the highest dissimilarity coefficient (0.893 yet to be reported among accessions. An analysis of molecular variance (AMOVA revealed that the greatest variation is within populations (87.8%, followed by the variation among populations (7.88%. The PhiST value (0.121 indicated moderate differentiation between populations. However, a spatial AMOVA (SAMOVA detected a stronger genetic structure of populations, with a PhiST value of 0.176. To understand the fine structure of populations, an analysis of data with Bayesian statistics was conducted with software Structure©. The number of genetic populations (K was five, with mixed ancestry in most individuals (genetic migrants, except in the Soconusco, where there was a tiny fraction of fragments from other populations. In contrast, SAMOVA grouped populations in four units. To corroborate the above findings, we searched for possible genetic barriers, determining as the main barrier that separating the Border from the rest of the populations. The results are discussed based on the possible ancestry of populations.

  7. Significance of population centers as sources of gaseous and dissolved PAHs in the lower Great Lakes.

    Science.gov (United States)

    McDonough, Carrie A; Khairy, Mohammed A; Muir, Derek C G; Lohmann, Rainer

    2014-07-15

    Polyethylene passive samplers (PEs) were used to measure concentrations of gaseous and dissolved polycyclic aromatic hydrocarbons (PAHs) in the air and water throughout the lower Great Lakes during summer and fall of 2011. Atmospheric Σ15PAH concentrations ranged from 2.1 ng/m3 in Cape Vincent (NY) to 76.4 ng/m3 in downtown Cleveland (OH). Aqueous Σ18PAH concentrations ranged from 2.4 ng/L at an offshore Lake Erie site to 30.4 ng/L in Sheffield Lake (OH). Gaseous PAH concentrations correlated strongly with population within 3-40 km of the sampling site depending on the compound considered, suggesting that urban centers are a primary source of gaseous PAHs (except retene) in the lower Great Lakes region. The significance of distant population (within 20 km) versus local population (within 3 km) increased with subcooled liquid vapor pressure. Most dissolved aqueous PAHs did not correlate significantly with population, nor were they consistently related to river discharge, wastewater effluents, or precipitation. Air-water exchange calculations implied that diffusive exchange was a source of phenanthrene to surface waters, while acenaphthylene volatilized out of the lakes. Comparison of air-water fluxes with temperature suggested that the significance of urban centers as sources of dissolved PAHs via diffusive exchange may decrease in warmer months.

  8. Loss and recovery of genetic diversity in adapting populations of HIV.

    Directory of Open Access Journals (Sweden)

    Pleuni S Pennings

    2014-01-01

    Full Text Available The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence data, we make four observations that shed a light on the underlying processes and allow us to infer the short-term effective population size of the viral population in a patient. Our first observation is that the evolution of drug resistance usually occurs by the fixation of one drug-resistance mutation at a time, as opposed to several changes simultaneously. Second, we find that these fixation events are accompanied by a reduction in genetic diversity in the region surrounding the fixed drug-resistance mutation, due to the hitchhiking effect. Third, we observe that the fixation of drug-resistance mutations involves both hard and soft selective sweeps. In a hard sweep, a resistance mutation arises in a single viral particle and drives all linked mutations with it when it spreads in the viral population, which dramatically reduces genetic diversity. On the other hand, in a soft sweep, a resistance mutation occurs multiple times on different genetic backgrounds, and the reduction of diversity is weak. Using the frequency of occurrence of hard and soft sweeps we estimate the effective population size of HIV to be 1.5 x 10(5 (95% confidence interval [0.8 x 10(5,4.8 x 10(5]. This number is much lower than the actual number of infected cells, but much larger than previous population size estimates based on synonymous diversity. We propose several explanations for the observed discrepancies. Finally, our fourth observation is that genetic diversity at non-synonymous sites recovers to its pre-fixation value within 18 months, whereas diversity at synonymous sites remains depressed after this time period. These results improve our understanding of HIV evolution and have potential implications for treatment strategies.

  9. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese...... geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...

  10. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean.

    Science.gov (United States)

    Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

    2013-02-01

    Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O(2) concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and 16S small subunit ribosomal RNA (16S rRNA) gene sequencing (clone libraries and 454-pyrotags). Estimates of MGA abundance as a proportion of total bacteria were similar across all three methods although estimates based on CARD-FISH were consistently lower in the OMZ (5.6%±1.9%) than estimates based on 16S rRNA gene clone libraries (11.0%±3.9%) or pyrotags (9.9%±1.8%). Five previously defined MGA subgroups were recovered in 16S rRNA gene clone libraries and five novel subgroups were defined (HF770D10, P262000D03, P41300E03, P262000N21 and A714018). Rarefaction analysis of pyrotag data indicated that the ultimate richness of MGA was very nearly sampled. Spearman's rank analysis of MGA abundances by CARD-FISH and O(2) concentrations resulted in significant correlation. Analyzed in more detail by 16S rRNA pyrotag sequencing, MGA operational taxonomic units affiliated with subgroups Arctic95A-2 and A714018 comprised 0.3-2.4% of total bacterial sequences and displayed strong correlations with decreasing O(2) concentration. This study is the first comprehensive description of MGA diversity using complementary techniques. These results provide a phylogenetic framework for interpreting future studies on ecotype selection among MGA subgroups, and suggest a potentially important role for MGA in the ecology and biogeochemistry of OMZs.

  11. Genetic diversity in three populations of Avicennia marina along the eastcoast of India by RAPD markers.

    Science.gov (United States)

    Hazarika, Dimendra; Thangaraj, M; Sahu, Sunil Kumar; Kathiresan, K

    2013-05-01

    Genetic diversity was analysed in three populations of the mangrove species, Avicennia marina by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Ten random decamer primers were used to score the diversity from three locations of eastcoast of India: Parangipettai (Tamil Nadu), Kakkinada (Andhra Pradesh) and Sundarbans (West Bengal). These primers produced 388 scorable DNA fragments, of which 252 (64.98%) were polymorphic, 182 (46.90%) were monomorphic, and 14 (3.61%) were unique. RAPD banding patterns displayed variations between and within the populations, while, there was no morphological variation.

  12. Genetic diversity and structure of domestic cavy (Cavia porcellus populations from smallholder farms in southern Cameroon

    Directory of Open Access Journals (Sweden)

    Basengere Ayagirwe

    2017-09-01

    Full Text Available Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wouri, Moungo and Nkongsamba in the Littoral region, and Mémé and Fako in the Southwest region of Cameroon. Twelve markers worked in the five populations with a total of 17 alleles identified, with a range of 2.9 to 4.0 alleles per locus. Observed heterozygosity (from 0.022 to 0.277 among populations was lower than expected heterozygosity (from 0.42 to 0.54. Inbreeding rates between individuals of the populations and between individuals in each population were 59.3% and 57.2%, respectively, against a moderate differentiation rate of 4.9%. All the tested loci deviated from Hardy-Weinberg equilibrium, except for locus 3. Genetic distances between populations were small (from 0.008 to 0.277, with a high rate of variability among individuals within each population (54.4%. Three distinct genetic groups were structured. This study has shown that microsatellites are useful for the genetic characterization of cavy populations in Cameroon and that the populations investigated have sufficient genetic diversity that can be used to be deployed as a basis for weight, prolificacy and disease resistance improvement. The genetic of diversity in Southern Cameroon is wide and constitute an opportunity for cavy breeding program.

  13. Danish Anti-Multiculturalism? The Significance of the Political Framing of Diversity

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2013-01-01

    , since the Danish state has never adopted an official multiculturalism policy and the criticism of multiculturalism has been dominant in public discourse for over a decade. Secondly, I will draw attention both to the quite different possible meanings of ‘multiculturalism’ and the different ways in which...... why these conceptual distinctions and empirical developments are normatively significant. In so doing, I will consider what is really at stake in debates over multiculturalism in a country like Denmark, suggesting that multiculturalism controversies are not only or primarily about the actual policies...... adopted, but concern the way in which policies are framed, the terms in which they are debated, and the ‘symbolic meaning’ with which they are thereby associated....

  14. Chemical diversity and pharmacological significance of the secondary metabolites of nutmeg (Myristica fragrans Houtt.).

    Science.gov (United States)

    Abourashed, Ehab A; El-Alfy, Abir T

    2016-12-01

    Nutmeg is a valued kitchen spice that has been used for centuries all over the world. In addition to its use in flavoring foods and beverages, nutmeg has been used in traditional remedies for stomach and kidney disorders. The antioxidant, antimicrobial and central nervous system effects of nutmeg have also been reported in literature. Nutmeg is a rich source of fixed and essential oil, triterpenes, and various types of phenolic compounds. Many of the secondary metabolites of nutmeg exhibit biological activities that may support its use in traditional medicine. This article provides an overview of the chemistry of secondary metabolites isolated from nutmeg kernel and mace including common methods for analysis of extracts and pure compounds as well as recent approaches towards total synthesis of some of the major constituents. A summary of the most significant pharmacological investigations of potential drug leads isolated from nutmeg and reported in the last decade is also included.

  15. Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

    Science.gov (United States)

    Zhang, Dapeng; Arevalo-Gardini, Enrique; Mischke, Sue; Zúñiga-Cernades, Luis; Barreto-Chavez, Alejandro; Del Aguila, Jorge Adriazola

    2006-09-01

    Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

  16. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    OpenAIRE

    Vangestel, C; Mergeay, Joachim; Dawson, D. A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierar...

  17. Temperature-associated population diversity in salmon confers benefits to mobile consumers

    Science.gov (United States)

    Ruff, Casey P.; Schindle, Daniel E.; Armstrong, Jonathan B.; Bentle, Kale T.; Brooks, Gabriel T.; Holtgrieve, Gordon W.; McGlauflin, Molly T.; Torgersen, Christian E.; Seeb, James E.

    2011-01-01

    Habitat heterogeneity can generate intraspecific diversity through local adaptation of populations. While it is becoming increasingly clear that population diversity can increase stability in species abundance, less is known about how population diversity can benefit consumers that can integrate across population diversity in their prey. Here we demonstrate cascading effects of thermal heterogeneity on trout–salmon interactions in streams where rainbow trout rely heavily on the seasonal availability of anadromous salmon eggs. Water temperature in an Alaskan stream varied spatially from 5°C to 17.5°C, and spawning sockeye salmon showed population differentiation associated with this thermal heterogeneity. Individuals that spawned early in cool regions of the 5 km long stream were genetically differentiated from those spawning in warmer regions later in the season. Sockeye salmon spawning generates a pulsed resource subsidy that supports the majority of seasonal growth in stream-dwelling rainbow trout. The spatial and temporal structuring of sockeye salmon spawn timing in our focal stream extended the duration of the pulsed subsidy compared to a thermally homogeneous stream with a single population of salmon. Further, rainbow trout adopted movement strategies that exploited the multiple pulses of egg subsidies in the thermally heterogeneous stream. Fish that moved to track the resource pulse grew at rates about 2.5 times higher than those that remained stationary or trout in the reference stream with a single seasonal pulse of eggs. Our results demonstrate that habitat heterogeneity can have important effects on the population diversity of dominant species, and in turn, influence their value to species that prey upon them. Therefore, habitat homogenization may have farther-reaching ecological effects than previously considered.

  18. Decline of heterozygosity in a large but isolated population: a 45-year examination of moose genetic diversity on Isle Royale

    Directory of Open Access Journals (Sweden)

    Renae L. Sattler

    2017-07-01

    Full Text Available Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces population on Isle Royale (Lake Superior from 1960–2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region. We also simulated the moose population to generate a theoretical backdrop of genetic diversity change. In the empirical data, we found that the number of alleles was consistently low and that observed heterozygosity notably declined from 1960 to 2005 (p = 0.08, R2 = 0.70. Furthermore, inbreeding coefficients approximately doubled from 0.08 in 1960–65 to 0.16 in 2000–05. Finally, we found that the empirical rate of observed heterozygosity decline was faster than the rate of observed heterozygosity loss in our simulations. Combined, these data suggest that genetic drift and inbreeding occurred in the Isle Royale moose populations over the study period, leading to significant losses in heterozygosity. Although inbreeding can be mitigated by migration, we found no evidence to support the occurrence of recent migrants into the population using analysis of our mtDNA haplotypes nor microsatellite data. Therefore, the Isle Royale moose population illustrates that even large populations are subjected to inbreeding in the absence of migration.

  19. Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

    Science.gov (United States)

    Dumitrescu, Logan; Carty, Cara L.; Taylor, Kira; Schumacher, Fredrick R.; Hindorff, Lucia A.; Ambite, José L.; Anderson, Garnet; Best, Lyle G.; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S.; Cochran, Barbara; Cole, Shelley A.; Devereux, Richard B.; Duggan, Dave; Eaton, Charles B.; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V.; Johnson, Karen C.; Laston, Sandra; Kolonel, Laurence N.; Lee, Elisa T.; MacCluer, Jean W.; Manolio, Teri A.; Pendergrass, Sarah A.; Quibrera, Miguel; Shohet, Ralph V.; Wilkens, Lynne R.; Haiman, Christopher A.; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E.; Crawford, Dana C.

    2011-01-01

    For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS–identified variants in diverse population-based studies. We genotyped 49 GWAS–identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (∼20,000), African American (∼9,000), American Indian (∼6,000), Mexican American/Hispanic (∼2,500), Japanese/East Asian (∼690), and Pacific Islander/Native Hawaiian (∼175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits. PMID:21738485

  20. Racial characterization and genetic diversity of sunflower broomrape populations from Northern Spain

    Directory of Open Access Journals (Sweden)

    Jebri MALEK

    2017-05-01

    Full Text Available In Spain, sunflower broomrape (Orobanche cumana Wallr. has been restricted to Cuenca province in Central Spain, and the Guadalquivir Valley in Southern Spain, that represent different gene pools of the species. This pathogenic plant has now spread to other areas such as Castilla y León region in Northern Spain. The racial status and genetic diversity were investigated in six populations of sunflower broomrape collected in several provinces of Castilla y León. Evaluation of virulence to a set of differential host genotypes classified three of the populations as race F, while the other three populations were classified as a race below F, probably race E. Genetic diversity analysis using a set of 20 SSR markers showed that the broomrape populations from new areas of Northern Spain are mainly derived from the Guadalquivir Valley gene pool. Introgression from the Cuenca gene pool was observed in one of the populations, in which the percentage of polymorphic loci was 31%, Shanon´s diversity index was 0.17, and the average number of pairwise differences was 1.69, compared to zero for the three parameters in the other five populations. The absence of race F individuals in the populations classified as race below F indicated that seed migration took place, probably before the generalized expansion of race F in the Guadalquivir Valley area, at the beginning of the 1990s.

  1. Genetic Diversity and Structure among Isolated Populations of the Endangered Gees Golden Langur in Assam, India

    Science.gov (United States)

    Biswas, Jihosuo; Nag, Sudipta; Shil, Joydeep; Umapathy, Govindhaswamy

    2016-01-01

    Gee’s golden langur (Trachypithecus geei) is an endangered colobine primate, endemic to the semi-evergreen and mixed-deciduous forests of Indo-Bhutan border. During the last few decades, extensive fragmentation has caused severe population decline and local extinction of golden langur from several fragments. However, no studies are available on the impact of habitat fragmentation and the genetic diversity of golden langur in the fragmented habitats. The present study aimed to estimate the genetic diversity in the Indian population of golden langur. We sequenced and analyzed around 500 bases of the mitochondrial DNA (mtDNA) hypervariable region-I from 59 fecal samples of wild langur collected from nine forest fragments. Overall, genetic diversity was high (h = 0.934, π = 0.0244) and comparable with other colobines. Populations in smaller fragments showed lower nucleotide diversity compared to the larger forest fragments. The median-joining network of haplotypes revealed a genetic structure that corresponded with the geographical distribution. The Aie and Champabati Rivers were found to be a barrier to gene flow between golden langur populations. In addition, it also established that T. geei is monophyletic but revealed possible hybridization with capped langur, T. pileatus, in the wild. It is hoped that these findings would result in a more scientific approach towards managing the fragmented populations of this enigmatic species. PMID:27564405

  2. Children with hemodynamically significant congenital heart disease can be identified through population-based registers

    DEFF Research Database (Denmark)

    Bergman, Gunnar; Hærskjold, Ann; Stensballe, Lone Graff

    2015-01-01

    BACKGROUND: Epidemiological research is facilitated in Sweden by a history of national health care registers, making large unselected national cohort studies possible. However, for complex clinical populations, such as children with congenital heart disease (CHD), register-based studies...... are challenged by registration limitations. For example, the diagnostic code system International Classification of Diseases, 10th version (ICD-10) does not indicate the clinical significance of abnormalities, therefore may be of limited use if used as the sole parameter in epidemiological research. Palivizumab...

  3. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

    Science.gov (United States)

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-09-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

  4. Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome.

    Science.gov (United States)

    Mukherjee, Souvik; Mitra, Rupak; Maitra, Arindam; Gupta, Satyaranjan; Kumaran, Srikala; Chakrabortty, Amit; Majumder, Partha P

    2016-10-27

    The skin microbiome varies across individuals. The causes of these variations are inadequately understood. We tested the hypothesis that inter-individual variation in facial skin microbiome can be significantly explained by variation in sebum and hydration levels in specific facial regions of humans. We measured sebum and hydration from forehead and cheek regions of healthy female volunteers (n = 30). Metagenomic DNA from skin swabs were sequenced for V3-V5 regions of 16S rRNA gene. Altogether, 34 phyla were identified; predominantly Actinobacteria (66.3%), Firmicutes (17.7%), Proteobacteria (13.1%) and Bacteroidetes (1.4%). About 1000 genera were identified; predominantly Propionibacterium (58.6%), Staphylococcus (8.6%), Streptococcus (4.0%), Corynebacterium (3.6%) and Paracoccus (3.3%). A subset (n = 24) of individuals were sampled two months later. Stepwise multiple regression analysis showed that cheek sebum level was the most significant predictor of microbiome composition and diversity followed by forehead hydration level; forehead sebum and cheek hydration levels were not. With increase in cheek sebum, the prevalence of Actinobacteria (p = 0.001)/Propionibacterium (p = 0.002) increased, whereas microbiome diversity decreased (Shannon Index, p = 0.032); this was opposite for other phyla/genera. These trends were reversed for forehead hydration levels. Therefore, the nature and diversity of facial skin microbiome is jointly determined by site-specific lipid and water levels in the stratum corneum.

  5. Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective

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    Jobling Mark A

    2007-07-01

    Full Text Available Abstract Background The geographic and ethnolinguistic differentiation of many African Y-chromosomal lineages provides an opportunity to evaluate human migration episodes and admixture processes, in a pan-continental context. The analysis of the paternal genetic structure of Equatorial West Africans carried out to date leaves their origins and relationships unclear, and raises questions about the existence of major demographic phenomena analogous to the large-scale Bantu expansions. To address this, we have analysed the variation of 31 binary and 11 microsatellite markers on the non-recombining portion of the Y chromosome in Guinea-Bissau samples of diverse ethnic affiliations, some not studied before. Results The Guinea-Bissau Y chromosome pool is characterized by low haplogroup diversity (D = 0.470, sd 0.033, with the predominant haplogroup E3a*-M2 shared among the ethnic clusters and reaching a maximum of 82.2% in the Mandenka people. The Felupe-Djola and Papel groups exhibit the highest diversity of lineages and harbor the deep-rooting haplogroups A-M91, E2-M75 and E3*-PN2, typical of Sahel's more central and eastern areas. Their genetic distinction from other groups is statistically significant (P = 0.01 though not attributable to linguistic, geographic or religious criteria. Non sub-Saharan influences were associated with the presence of haplogroup R1b-P25 and particular lineages of E3b1-M78. Conclusion The predominance and high diversity of haplogroup E3a*-M2 suggests a demographic expansion in the equatorial western fringe, possibly supported by a local agricultural center. The paternal pool of the Mandenka and Balanta displays evidence of a particularly marked population growth among the Guineans, possibly reflecting the demographic effects of the agriculturalist lifestyle and their putative relationship to the people that introduced early cultivation practices into West Africa. The paternal background of the Felupe-Djola and Papel

  6. Filamentous fungal population and species diversity from the continental slope of Bay of Bengal, India

    Science.gov (United States)

    Das, Surajit; Lyla, Parameswari Somasundharan; Khan, Syed Ajmal

    2009-03-01

    Filamentous fungal diversity from the sediments of the continental slope of Bay of Bengal was studied. Sediment samples were collected during two voyages in 2004 and 2005. Filamentous fungal population from both the cruises showed a range of 5.17-59.51 CFU/g and 3.47-29.68 CFU/g, respectively. Totally 16 fungal genera were recorded from both the cruises. Aspergillus was found to be the dominant genus and the overall percentage occurrence was as follows: Deuteromycotina 74%, Ascomycotina 17%, Basidiomycotina 4% and non-sporulating 5%. Diversity indices were calculated and during both the cruises species richness ( d) varied from 0.912 to 3.622 and 1.443 to 4.588; evenness ( J') varied from 0.9183 to 1.000 and 0.8322 to 1.000 and Shannon-Wiener index ( H' log 2) varied from 0.9183 to 1.000 and 1.000 to 3.690. The higher diversity was found in Divipoint transect (northern Bay of Bengal). 95% confidence interval and ellipse showed that the stations were well lying within the funnel. Cluster analysis and MDS grouped the northern transects which showed higher diversity. BVSTEP resulted in isolation of 23 species which were most influential in the marine filamentous fungal diversity of the continental slope of Bay of Bengal. Thus, a lower population range and higher diversity of marine filamentous marine fungi in the sediments of the continental slope of Bay of Bengal was recorded.

  7. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

    OpenAIRE

    Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

    2012-01-01

    Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O2 concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and ...

  8. Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria

    Science.gov (United States)

    2005-06-01

    1973. Ecology of Vibrio parahemolyticus in mixed-template amplifications: formation, consequences and elimination by Chesapeake Bay. J. Bacteriol. 113...Science 1930 and Engineering DOCTORAL DISSERTATION Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria by...DYNAMICS IN NATURAL POPULATIONS OF PLANKTONIC VIBRIO BACTERIA by Janelle Ren6e Thompson B.S. Biological Sciences, Stanford University 1998 M.S

  9. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations.

    Science.gov (United States)

    Crawford, Andrew J; Cruz, Catalina; Griffith, Edgardo; Ross, Heidi; Ibáñez, Roberto; Lips, Karen R; Driskell, Amy C; Bermingham, Eldredge; Crump, Paul

    2013-11-01

    Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community. © 2012 John Wiley & Sons Ltd.

  10. Processes shaping gut microbiota diversity in allopatric populations of the endemic lizard Podarcis lilfordi from Menorcan islets (Balearic Islands).

    Science.gov (United States)

    Baldo, Laura; Riera, Joan Lluís; Mitsi, Konstantina; Pretus, Joan Lluís

    2018-02-01

    Compositional variation of the gut microbiota across host allopatric populations can reflect both adaptation and stochasticity since the time of separation. Major factors shaping this variation include the host phylogeographic and demographic history, the microbiota inheritance, environmental inputs and dispersal of bacteria. Here we explored the impact of these factors in driving gut community diversity in seven allopatric populations of the omnivorous lizard Podarcis lilfordi from the Menorcan coastal islets, all descending from an ancestral mainland population. Using 16S rRNA Illumina sequencing, we showed that 'islet' and 'age' (time since islet separation from mainland) were the only significant variables in microbial community clustering, suggesting a partial islet-restricted diversification following these lizards phylogeography. Despite a significant variation, islets/populations were characterized by a remarkably low bacterial uniqueness (2.4% of total OTUs) and a minor differential enrichment of taxa, indicating a negligible impact of local inputs and important host common constraints. Overall, the extant pattern of similarity/dissimilarity among islets is compatible with partial retention of the ancestral mainland microbial pool, with differences among islets potentially explained by a differential loss of bacteria following population fragmentation and bottlenecks (i.e. ecological drift). While more quantitative data are needed to validate this hypothesis, this study unveils the importance of considering both neutral and niche-driven processes in driving contemporary patterns of gut metacommunity diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Genotypic diversity of merozoite surface antigen 1 of Babesia bovis within an endemic population.

    Science.gov (United States)

    Lau, Audrey O T; Cereceres, Karla; Palmer, Guy H; Fretwell, Debbie L; Pedroni, Monica J; Mosqueda, Juan; McElwain, Terry F

    2010-08-01

    Multiple genetically distinct strains of a pathogen circulate and compete for dominance within populations of animal reservoir hosts. Understanding the basis for genotypic strain structure is critical for predicting how pathogens respond to selective pressures and how shifts in pathogen population structure can lead to disease outbreaks. Evidence from related Apicomplexans such as Plasmodium, Toxoplasma, Cryptosporidium and Theileria suggests that various patterns of population dynamics exist, including but not limited to clonal, oligoclonal, panmictic and epidemic genotypic strain structures. In Babesia bovis, genetic diversity of variable merozoite surface antigen (VMSA) genes has been associated with disease outbreaks, including in previously vaccinated animals. However, the extent of VMSA diversity within a defined population in an endemic area has not been examined. We analyzed genotypic diversity and temporal change of MSA-1, a member of the VMSA family, in individual infected animals within a reservoir host population. Twenty-eight distinct MSA-1 genotypes were identified within the herd. All genotypically distinct MSA-1 sequences clustered into three groups based on sequence similarity. Two thirds of the animals tested changed their dominant MSA-1 genotypes during a 6-month period. Five animals within the population contained multiple genotypes. Interestingly, the predominant genotypes within those five animals also changed over the 6-month sampling period, suggesting ongoing transmission or emergence of variant MSA-1 genotypes within the herd. This study demonstrated an unexpected level of diversity for a single copy gene in a haploid genome, and illustrates the dynamic genotype structure of B. bovis within an individual animal in an endemic region. Co-infection with multiple diverse MSA-1 genotypes provides a basis for more extensive genotypic shifts that characterizes outbreak strains.

  12. EvoSNP-DB: A database of genetic diversity in East Asian populations.

    Science.gov (United States)

    Kim, Young Uk; Kim, Young Jin; Lee, Jong-Young; Park, Kiejung

    2013-08-01

    Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

  13. Genetic Diversity and Population Differentiation of the Causal Agent of Citrus Black Spot in Brazil

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    Ester Wickert

    2012-01-01

    Full Text Available One of the most important diseases that affect sweet orange orchards in Brazil is the Citrus Black Spot that is caused by the fungus Guignardia citricarpa. This disease causes irreparable losses due to the premature falling of fruit, as well as its severe effects on the epidermis of ripe fruit that renders them unacceptable at the fresh fruit markets. Despite the fact that the fungus and the disease are well studied, little is known about the genetic diversity and the structure of the fungi populations in Brazilian orchards. The objective of this work was study the genetic diversity and population differentiation of G. citricarpa associated with four sweet orange varieties in two geographic locations using DNA sequence of ITS1-5.8S-ITS2 region from fungi isolates. We observed that different populations are closely related and present little genetic structure according to varieties and geographic places with the highest genetic diversity distributed among isolates of the same populations. The same haplotypes were sampled in different populations from the same and different orange varieties and from similar and different origins. If new and pathogenic fungi would become resistant to fungicides, the observed genetic structure could rapidly spread this new form from one population to others.

  14. Characterization of genetic diversity of native 'Ancho' chili populations of Mexico using microsatellite markers

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    Rocío Toledo-Aguilar

    2016-03-01

    Full Text Available 'Ancho' type chilis (Capsicum annuum L. var. annuum are an important ingredient in the traditional cuisine of Mexico and so are in high demand. It includes six native sub-types with morphological and fruit color differences. However, the genetic diversity of the set of these sub­types has not been determined. The objective of this study was to characterize the genetic diversity of native Mexican ancho chili populations using microsatellites and to determine the relationship among these populations. Twenty-four microsatellite loci were used to analyze 38 native populations of 'Ancho' chilis collected in seven states of Mexico; three populations different from the ancho type ('Piquin', 'Guajillo', and 'Chilaca' and three hybrids (Capulin, Abedul, and green pepper were included as controls. The number of alleles per locus, number and percentage of polymorphic loci, polymorphic information content (PIC, expected heterozygosity, and Wright F statistics were obtained. Moreover, an analysis of principal components and a cluster analysis were carried out. We detected 220 alleles, with an average of 9.2 alleles per locus; PIC varied between 0.07 and 1, and expected heterozygosity was between 0.36 and 0.59. Also we identified 59 unique alleles and eight alleles common to all of the populations. The F statistics revealed broad genetic differentiation among populations. Both the analysis of principal components and the cluster analysis were able to separate the populations by origin (southern, central, and northern Mexico. The broad genetic diversity detected in the native ancho chili populations of Mexico was found in greater proportion within the populations than between populations.

  15. Food addiction: its prevalence and significant association with obesity in the general population.

    Science.gov (United States)

    Pedram, Pardis; Wadden, Danny; Amini, Peyvand; Gulliver, Wayne; Randell, Edward; Cahill, Farrell; Vasdev, Sudesh; Goodridge, Alan; Carter, Jacqueline C; Zhai, Guangju; Ji, Yunqi; Sun, Guang

    2013-01-01

    'Food addiction' shares a similar neurobiological and behavioral framework with substance addiction. However whether, and to what degree, 'food addiction' contributes to obesity in the general population is unknown. to assess 1) the prevalence of 'food addiction' in the Newfoundland population; 2) if clinical symptom counts of 'food addiction' were significantly correlated with the body composition measurements; 3) if food addicts were significantly more obese than controls, and 4) if macronutrient intakes are associated with 'food addiction'. A total of 652 adults (415 women, 237 men) recruited from the general population participated in this study. Obesity was evaluated by Body Mass Index (BMI) and Body Fat percentage measured by dual-energy X-ray absorptiometry. 'Food addiction' was assessed using the Yale Food Addiction Scale and macronutrient intake was determined from the Willet Food Frequency Questionnaire. The prevalence of 'food addiction' was 5.4% (6.7% in females and 3.0% in males) and increased with obesity status. The clinical symptom counts of 'food addiction' were positively correlated with all body composition measurements across the entire sample (pObesity measurements were significantly higher in food addicts than controls; Food addicts were 11.7 (kg) heavier, 4.6 BMI units higher, and had 8.2% more body fat and 8.5% more trunk fat. Furthermore, food addicts consumed more calories from fat and protein compared with controls. Our results demonstrated that 'food addiction' contributes to severity of obesity and body composition measurements from normal weight to obese individuals in the general population with higher rate in women as compared to men.

  16. Genetic diversity of Bemisia tabaci (Genn. Populations in Brazil revealed by RAPD markers

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    L.H.C. Lima

    2002-01-01

    Full Text Available Bemisia tabaci (Genn. was considered a secondary pest in Brazil until 1990, despite being an efficient geminivirus vector in beans and soybean. In 1991, a new biotype, known as B. tabaci B biotype (=B. argentifolii was detected attacking weed plants and causing phytotoxic problems in Cucurbitaceae. Nowadays, B. tabaci is considered one of the most damaging whitefly pests in agricultural systems worldwide that transmits more than 60 different plant viruses. Little is known about the genetic variability of these populations in Brazil. Knowledge of the genetic variation within whitefly populations is necessary for their efficient control and management. The objectives of the present study were to use RAPD markers (1 to estimate the genetic diversity of B. tabaci populations, (2 to study the genetic relationships among B. tabaci biotypes and two other whitefly species and (3 to discriminate between B. tabaci biotypes. A sample of 109 B. tabaci female individuals obtained from 12 populations in Brazil were analyzed and compared to the A biotype from Arizona (USA and B biotype from California (USA and Paraguay. Trialeurodes vaporariorum and Aleurodicus cocois samples were also included. A total of 72 markers were generated by five RAPD primers and used in the analysis. All primers produced RAPD patterns that clearly distinguished the Bemisia biotypes and the two other whitefly species. Results also showed that populations of the B biotype have considerable genetic variability. An average Jaccard similarity of 0.73 was observed among the B biotype individuals analyzed. Cluster analysis demonstrated that, in general, Brazilian biotype B individuals are scattered independently in the localities where samples were collected. Nevertheless, some clusters were evident, joining individuals according to the host plants. AMOVA showed that most of the total genetic variation is found within populations (56.70%, but a significant portion of the variation is found

  17. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana).

    Science.gov (United States)

    Shih, Kai-Ming; Chang, Chung-Te; Chung, Jeng-Der; Chiang, Yu-Chung; Hwang, Shih-Ying

    2018-01-01

    Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana , disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, F ST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana . Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana , but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana , was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population

  18. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana

    Directory of Open Access Journals (Sweden)

    Kai-Ming Shih

    2018-02-01

    Full Text Available Double digest restriction site-associated DNA sequencing (ddRADseq is a tool for delivering genome-wide single nucleotide polymorphism (SNP markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals of K. davidiana var. formosana. Principal component analysis (PCA, individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE. However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals. This study has produced highly informative population genomic data for the understanding of

  19. Characterization of MHC-I in the blue tit (Cyanistes caeruleus) reveals low levels of genetic diversity and trans-population evolution across European populations.

    Science.gov (United States)

    Schut, Elske; Aguilar, Juan Rivero-de; Merino, Santiago; Magrath, Michael J L; Komdeur, Jan; Westerdahl, Helena

    2011-08-01

    The major histcompatibility complex (MHC) is a vital component of the adaptive immune system in all vertebrates. This study is the first to characterize MHC class I (MHC-I) in blue tits (Cyanistes caeruleus), and we use MHC-I exon 3 sequence data from individuals originating from three locations across Europe: Spain, the Netherlands to Sweden. Our phylogeny of the 17 blue tit MHC-I alleles contains one allele cluster with low nucleotide diversity compared to the remaining more diverse alleles. We found a significant evidence for balancing selection in the peptide-binding region in the diverse allele group only. No separation according to geographic location was found in the phylogeny of alleles. Although the number of MHC-I loci of the blue tit is comparable to that of other passerine species, the nucleotide diversity of MHC-I appears to be much lower than that of other passerine species, including the closely related great tit (Parus major) and the severely inbred Seychelles warbler (Acrocephalus sechellensis). We believe that this initial MHC-I characterization in blue tits provides an important step towards understanding the mechanisms shaping MHC-I diversity in natural populations.

  20. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

    Science.gov (United States)

    The diversity and population-genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analyzed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, Romagnola), sequenced to 11-fold...

  1. Comparison of recruitment and retention among demographic subgroups in a large diverse population study of diet

    Directory of Open Access Journals (Sweden)

    Gwen L. Alexander, PhD

    2017-06-01

    Conclusions: While study recruitment remains challenging, once recruited most participants, regardless of race/ethnicity, completed two 24-h dietary recalls, both interviewer-administered and self-administered on the web. This study demonstrates the feasibility of collecting multiple 24-h recalls including less expensive automated self-administered recalls among diverse populations.

  2. Bullying in an Increasingly Diverse School Population: A Socio-Ecological Model Analysis

    Science.gov (United States)

    Lim, Seok Jeng Jane; Hoot, James L.

    2015-01-01

    Systematic research into bullying has a short history spanning about 40 years. However, investigations into school bullying from a multicultural context are especially limited. As schools in the 21st century become increasingly diverse due to rapid globalization and immigration, there is a need to consider bullying within changing populations. The…

  3. Population diversity of Diaphorina citri (Hemiptera: Liviidae) in China based on whole mitochondrial genome sequences

    Science.gov (United States)

    BACKGROUND: Diaphorina citri (Asian citrus psyllid, ACP) transmits “Candidatus Liberibacter asiaticus”, an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). ACP has been reported in 11 provinces/regions in China, yet its population diversity remains unclear. In this stud...

  4. Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

    Science.gov (United States)

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  5. Intercultural Leadership Toolkit for Librarians: Building Awareness to Effectively Serve Diverse Multicultural Populations

    Science.gov (United States)

    Allard, Suzie; Mehra, Bharat; Qayyum, M. Asim

    2007-01-01

    This paper presents five tools for librarians to use in building effective intercultural communication that reaches out to diverse populations. Librarians can more successfully cross intercultural boundaries if they are aware of the key tenets of intercultural communication and information provision, and then apply the five leadership tools in…

  6. Genetic diversity and population structure of a protected species: Polygala tenuifolia Willd.

    Science.gov (United States)

    Peng, Yan Qun; Fan, Ling Ling; Mao, Fu Ying; Zhao, Yun Sheng; Xu, Rui; Yin, Yu Jie; Chen, Xin; Wan, De Guang; Zhang, Xin Hui

    2018-03-01

    Polygala tenuifolia Willd. is an important protected species used in traditional Chinese medicine. In the present study, amplified fragment length polymorphism (AFLP) markers were employed to characterize the genetic diversity in wild and cultivated P. tenuifolia populations. Twelve primer combinations of AFLP produced 310 unambiguous and repetitious bands. Among these bands, 261 (84.2%) were polymorphic. The genetic diversity was high at the species level: percentage of polymorphic loci (PPL)=84.2%, Nei's gene diversity (h)=0.3296 and Shannon's information index (I)=0.4822. Between the two populations, the genetic differentiation of 0.1250 was low and the gene flow was relatively high, at 3.4989. The wild population (PPL=81.9%, h=0.3154, I=0.4635) showed a higher genetic diversity level than the cultivated population (PPL=63.9%, h=0.2507, I=0.3688). The results suggest that the major factors threatening the persistence of P. tenuifolia resources are ecological and human factors rather than genetic. These results will assist with the design of conservation and management programs, such as in natural habitat conservation, setting the excavation time interval for resource regeneration and the substitution of cultivated for wild plants. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

  7. Microsatellite variability in the entomopathogenic fungus Paeciolomyces fumosoroseus: genetic diversity and population structure

    Science.gov (United States)

    The hyphomycete Paecilomyces fumosoroseus (Pfr) is a geographically widespread fungus capable of infecting various insect hosts. The fungus has been used for the biological control of several important insect pests of agriculture. However knowledge of the fungus’ genetic diversity and population str...

  8. Parental Opinion Concerning School Sexuality Education in a Culturally Diverse Population in the USA

    Science.gov (United States)

    Heller, Janet R.; Johnson, Helen L.

    2013-01-01

    This study aimed to expand upon previous research related to parental opinion concerning school sexuality education by sampling a culturally diverse, low-income population that has been traditionally under-represented in the literature. A total of 191 parents attending an urban community college completed a written questionnaire about what topics…

  9. Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand.

    Science.gov (United States)

    Pattaradilokrat, Sittiporn; Sawaswong, Vorthon; Simpalipan, Phumin; Kaewthamasorn, Morakot; Siripoon, Napaporn; Harnyuttanakorn, Pongchai

    2016-10-21

    An effective malaria vaccine is an urgently needed tool to fight against human malaria, the most deadly parasitic disease of humans. One promising candidate is the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum. This antigenic protein, encoded by the merozoite surface protein (msp-3) gene, is polymorphic and classified according to size into the two allelic types of K1 and 3D7. A recent study revealed that both the K1 and 3D7 alleles co-circulated within P. falciparum populations in Thailand, but the extent of the sequence diversity and variation within each allelic type remains largely unknown. The msp-3 gene was sequenced from 59 P. falciparum samples collected from five endemic areas (Mae Hong Son, Kanchanaburi, Ranong, Trat and Ubon Ratchathani) in Thailand and analysed for nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity. The gene was also subject to population genetic analysis (F st ) and neutrality tests (Tajima's D, Fu and Li D* and Fu and Li' F* tests) to determine any signature of selection. The sequence analyses revealed eight unique DNA haplotypes and seven amino acid sequence variants, with a haplotype and nucleotide diversity of 0.828 and 0.049, respectively. Neutrality tests indicated that the polymorphism detected in the alanine heptad repeat region of MSP-3 was maintained by positive diversifying selection, suggesting its role as a potential target of protective immune responses and supporting its role as a vaccine candidate. Comparison of MSP-3 variants among parasite populations in Thailand, India and Nigeria also inferred a close genetic relationship between P. falciparum populations in Asia. This study revealed the extent of the msp-3 gene diversity in P. falciparum in Thailand, providing the fundamental basis for the better design of future blood stage malaria vaccines against P. falciparum.

  10. Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation.

    Science.gov (United States)

    Morgan, Matthew J; Hunter, David; Pietsch, Rod; Osborne, William; Keogh, J Scott

    2008-08-01

    The iconic and brightly coloured Australian northern corroboree frog, Pseudophryne pengilleyi, and the southern corroboree frog, Pseudophryne corroboree are critically endangered and may be extinct in the wild within 3 years. We have assembled samples that cover the current range of both species and applied hypervariable microsatellite markers and mitochondrial DNA sequences to assess the levels and patterns of genetic variation. The four loci used in the study were highly variable, the total number of alleles observed ranged from 13 to 30 and the average number of alleles per locus was 19. Expected heterozygosity of the four microsatellite loci across all populations was high and varied between 0.830 and 0.935. Bayesian clustering analyses in STRUCTURE strongly supported four genetically distinct populations, which correspond exactly to the four main allopatric geographical regions in which the frogs are currently found. Individual analyses performed on the separate regions showed that breeding sites within these four regions could not be separated into distinct populations. Twelve mtND2 haplotypes were identified from 66 individuals from throughout the four geographical regions. A statistical parsimony network of mtDNA haplotypes shows two distinct groups, which correspond to the two species of corroboree frog, but with most of the haplotype diversity distributed in P. pengilleyi. These results demonstrate an unexpectedly high level of genetic diversity in both species. Our data have important implications for how the genetic diversity is managed in the future. The four evolutionarily significant units must be protected and maintained in captive breeding programmes for as long as it is possible to do.

  11. Genetic diversity of Iranian honey bee (Apis mellifera meda Skorikow, 1829) populations based on ISSR markers.

    Science.gov (United States)

    Rahimi, A; Mirmoayedi, A; Kahrizi, D; Zarei, L; Jamali, S

    2016-04-30

    Honey bee is one of the most important insects considering its role in agriculture,ecology and economy as a whole. In this study, the genetic diversity of different Iranian honey bee populations was evaluated using inter simple sequence repeat (ISSR) markers. During May to September 2014, 108 young worker honey bees were collected from six different populations in 30 different geoclimatic locations from Golestan, Mazendaran, Guilan, West Azerbaijan, East Azerbaijan, Ardebil provinces of Iran. DNA was extracted from the worker honey bees. The quality and quantity of extracted DNA were measured. A set of ten primers were screened with the laboratory populations of honey bees. The number of fragments produced in the different honey bee populations varied from 3 to 10, varying within 150 to 1500 bp. The used ten ISSR primers generated 40 polymorphic fragments, and the average heterozygosity for each primer was 0.266. Maximum numbers of bands were recorded for primer A1. A dendrogram based on the Unweighted Pair Group Method with Arithmetic mean (UPGMA) method generated two sub-clusters. Honey bee populations of Golestan, Mazendaran, Guilan provinces were located in the first group. The second group included honey bee populations of Ardebil, West Azerbaijan, East Azerbaijan provinces, but this group showed a close relationship with other populations. The results showed obviously the ability of the ISSR marker technique to detect the genetic diversity among the honey bee populations.

  12. Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

    Science.gov (United States)

    Demers, Jill E.; Gugino, Beth K.

    2014-01-01

    The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates. PMID:25304514

  13. Diversity of palatal rugae patterns and their reliability in sex discrimination in a South Indian population

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    Sai Madhavi Nallamilli

    2015-01-01

    Full Text Available Introduction and Aims: Array of palatal rugae in the realm of forensic odontology has been constantly explored owing to their individual uniqueness and resistance to postmortem procedures, while their scope in sex determination and racial profiling remains understated. In this context, the present study aimed to record the diversity of palatal rugae patterns in a South Indian population. Materials and Methods: A descriptive cross-sectional study was conducted among people who reported to the outpatient department of a dental institution. Sample comprised a total of 200 subjects divided into two groups of 100 each, based upon gender. Impressions of anterior maxilla were made of all the study subjects and casts obtained subsequently. Outline of palatal rugae pattern was traced on these models and the data computed. Z test and unpaired t-test were used for statistical analysis and the probability value calculated. In addition, logistic regression analysis was performed to estimate the accuracy of sex allocation. Results: The shape of rugae exhibited highly significant sex difference in the curved type, which was found to be higher in males, and in the wavy type which was higher in females, enabling sex differentiation using palatal rugae patterns. Logistic regression analysis predicted high power of sex allocation for males rather than females in the study population. Conclusion: This study highlighted the uniqueness and greater sex discrimination potential of curved shape of palatal rugae in categorizing males of South Indian population, substantiating their use in the identification of deceased, by relating the antemortem and postmortem dental records.

  14. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.

    Science.gov (United States)

    Remnant, Emily J; Shi, Mang; Buchmann, Gabriele; Blacquière, Tjeerd; Holmes, Edward C; Beekman, Madeleine; Ashe, Alyson

    2017-08-15

    Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees ( Apis mellifera ) has changed dramatically since the emergence of the parasitic mite Varroa destructor , which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa -infected colonies are often overwhelmed

  15. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations

    Science.gov (United States)

    Shi, Mang; Buchmann, Gabriele; Blacquière, Tjeerd; Beekman, Madeleine; Ashe, Alyson

    2017-01-01

    ABSTRACT Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa. This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management. IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales. Collapsing Varroa-infected colonies are often

  16. Genetic structure and diversity of three Colombian southwest afrodescendent populations using 8 STR's

    International Nuclear Information System (INIS)

    Guauque Olarte, Sandra; Fuentes Pardo, Angela Patricia; Cardenas Henao, Heiber; Barreto, Guillermo

    2010-01-01

    To estimate the diversity, structure and genetic flow in three Colombian southwest afrodescendent populations (Buenaventura, Mulalo y Tumaco), the alleles revealed by 8 autosomal STR's were analyzed in 78 no-related individuals, by the use of PCR and comparison with specific allelic ladders for every system resolved by polyacrylamide gel (8%). the results were compared with 2 Amerindian populations (Awa-Kuaikier and Coyaima) and 2 mixed Colombian populations (Valle del Cauca and Cauca). For the afrodescendent and Amerindian populations was found moderate diversity (h between 0.768±0.414 and 0.796±0.424), in contrast, the mixed population showed higher rates (>0.803), which is probably caused by mixing with Amerindians, that also can explain the high endogamy seen in mixed populations. The AMOVA exhibited moderate genetic structure between the afrodescendent populations (FST= 0.098; p<0.05), but higher between the three ethnical groups compared (FST=0.26723; p<0.05). The closer genetics distances are in favor of Tumaco and Buenaventura, supported for the migration rate found (34.298), which was the same inside of Amerindian and mixed populations. Maybe, because Mulalo is a closed isolated population, its differences in front others afrodescendent populations are explained. The neighbor-joining tree showed nearest relations among Amerindian and mixed populations, furthermore, the ancestral character for the afrodescendents. That sustains the idea of genetic flow maintained between the 3 ethnical groups, principally between Amerindian and mixed populations, supported because the genetic differences, migration rates and Amerindian matrilineality reported in the literature

  17. Coronary artery disease in a rural population of Bangladesh: is dyslipidemia or adiposity a significant risk?

    Directory of Open Access Journals (Sweden)

    Sajal Krishna Banerjee

    2017-07-01

    Full Text Available Background and Aims: The prevalence of cardiovascular diseases (CVD are on the increase worldwide and more in the developing countries. Coronary artery disease (CAD constitutes the major brunt of CVD. Despite the increasing morbidity and mortality, Bangladesh has a few published data on CAD in rural population. This study addressed the prevalence of CAD and its risk factors in rural population of Bangladesh. Study methods: Sixteen villages were purposively selected in a rural area. A population census was conducted in the selected area. The census yielded eligible participants, who reached at least eighteen years of age. Those who willingly consented to participate were enlisted. Each participant was interviewed regarding CAD risk (age, sex, social class, occupation, illness, family history. Anthropometry (height, weight, waist- and hip-girth was recorded. Resting blood pressure (BP was measured. Blood sample was collected for fasting blood glucose (FBG, total cholesterol (Chol, triglycerides (Tg, low density lipoproteins (LDL, very low density lipoproteins (VLDL and high density (HDL. All participants having FBG>5.5mmol/l or systolic (SBP ³135 or diastolic BP (DBP ³85mmHg underwent electrocardiography (ECG. A team of cardiologists selected and accomplished exercise tolerance test (ETT and echocardiography (Echo. Results: The prevalence of CAD was 4.5% (95% CI: 3.85 – 5.15. Compared with the female (3.5%, CI, 2.76 – 4.24 the male participants had significantly higher prevalence of CAD (6.0%, CI, 4.83 – 7.13. Comparison of characteristics between participants with and without CAD showed that age, SBP, DBP and FBG were significantly higher in CAD group. Bivariate analysis showed that age, sex, social class, glycemic status, metabolic syndrome (MetS and smoking were significantly related to CAD. Stepwise logistic regression proved only male sex, rich social class, hypertension and diabetes had independent risk of CAD; whereas, age, obesity

  18. Host population genetic structure and zooxanthellae diversity of two reef-building coral species along the Florida Reef Tract and wider Caribbean

    Science.gov (United States)

    Baums, I. B.; Johnson, M. E.; Devlin-Durante, M. K.; Miller, M. W.

    2010-12-01

    In preparation for a large-scale coral restoration project, we surveyed host population genetic structure and symbiont diversity of two reef-building corals in four reef zones along the Florida reef tract (FRT). There was no evidence for coral population subdivision along the FRT in Acropora cervicornis or Montastraea faveolata based on microsatellite markers. However, in A. cervicornis, significant genetic differentiation was apparent when extending the analysis to broader scales (Caribbean). Clade diversity of the zooxanthellae differed along the FRT. A. cervicornis harbored mostly clade A with clade D zooxanthellae being prominent in colonies growing inshore and in the mid-channel zones that experience greater temperature fluctuations and receive significant nutrient and sediment input. M. faveolata harbored a more diverse array of symbionts, and variation in symbiont diversity among four habitat zones was more subtle but still significant. Implications of these results are discussed for ongoing restoration and conservation work.

  19. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm.

    Science.gov (United States)

    Lee, Hea-Young; Ro, Na-Young; Jeong, Hee-Jin; Kwon, Jin-Kyung; Jo, Jinkwan; Ha, Yeaseong; Jung, Ayoung; Han, Ji-Woong; Venkatesh, Jelli; Kang, Byoung-Cheorl

    2016-11-14

    Conservation of genetic diversity is an essential prerequisite for developing new cultivars with desirable agronomic traits. Although a large number of germplasm collections have been established worldwide, many of them face major difficulties due to large size and a lack of adequate information about population structure and genetic diversity. Core collection with a minimum number of accessions and maximum genetic diversity of pepper species and its wild relatives will facilitate easy access to genetic material as well as the use of hidden genetic diversity in Capsicum. To explore genetic diversity and population structure, we investigated patterns of molecular diversity using a transcriptome-based 48 single nucleotide polymorphisms (SNPs) in a large germplasm collection comprising 3,821 accessions. Among the 11 species examined, Capsicum annuum showed the highest genetic diversity (H E  = 0.44, I = 0.69), whereas the wild species C. galapagoense showed the lowest genetic diversity (H E  = 0.06, I = 0.07). The Capsicum germplasm collection was divided into 10 clusters (cluster 1 to 10) based on population structure analysis, and five groups (group A to E) based on phylogenetic analysis. Capsicum accessions from the five distinct groups in an unrooted phylogenetic tree showed taxonomic distinctness and reflected their geographic origins. Most of the accessions from European countries are distributed in the A and B groups, whereas the accessions from Asian countries are mainly distributed in C and D groups. Five different sampling strategies with diverse genetic clustering methods were used to select the optimal method for constructing the core collection. Using a number of allelic variations based on 48 SNP markers and 32 different phenotypic/morphological traits, a core collection 'CC240' with a total of 240 accessions (5.2 %) was selected from within the entire Capsicum germplasm. Compared to the other core collections, CC240 displayed higher

  20. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    Science.gov (United States)

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-12-09

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program.

  1. Phylogeography and population diversity of Simulium hirtipupa Lutz (Diptera: Simuliidae based on mitochondrial COI sequences.

    Directory of Open Access Journals (Sweden)

    Vanderly Andrade-Souza

    Full Text Available High morphological homogeneity and cryptic speciation may cause the diversity within Simuliidae to be underestimated. Recent molecular studies on population genetics and phylogeography have contributed to reveal which factors influenced the diversity within this group. This study aimed at examining the genetic diversity of Simulium hirtipupa Lutz, 1910 in populations from the biomes Caatinga, Cerrado, and Atlantic Forest. In this study, we carried out phylogeographic and population genetic analyses using a fragment of the mitochondrial gene COI. The 19 populations studied were clustered into seven groups, most of which are associated with geography indicating certain genetic structure. The northern region of the state of Minas Gerais is most likely the center of origin of this species. The average intergroup genetic distance was 3.7%, indicating the presence of cryptic species. The species tree as well as the haplotype network recovered all groups forming two major groups: the first comprises groups Gr-Bahia (in which the São Francisco river has not acted as geographical barrier, Gr-Pernambuco, and Gr-Mato Grosso do Sul. The second included groups comprising populations of the states of Goiás, Tocantins, Minas Gerais, Bahia, São Paulo, and Espírito Santo. The mismatch distribution for groups was consistent with the model of demographic expansion, except for the Gr-Central-East_1 group. The diversification in this group occurred about 1.19 Mya during the Pleistocene, influenced by paleoclimatic oscillations during the Quaternary glacial cycles.

  2. Significant association between RGS14 rs12654812 and nephrolithiasis risk among Guangxi population in China.

    Science.gov (United States)

    Long, Jun; Chen, Yang; Lin, Haisong; Liao, Ming; Li, Tianyu; Tong, Lei; Wei, Suchun; Xian, Xiaoying; Zhu, Jia; Chen, Jianxin; Tian, Jiarong; Wang, Qiuyan; Mo, Zengnan

    2018-03-26

    Nephrolithiasis is a worldwide health problem that affects almost all populations. This study aimed to evaluate the association between rs12654812 of regulator of G protein signaling 14 (RGS14) gene and nephrolithiasis in the Chinese population. A total of 1541 participators including 830 cases and 711 controls were included from Guangxi area in China. Age, sex, BMI, smoking status, drinking status, creatinine, uric acid, and urea nitrogen were analyzed between the case group and control group. We found that the G/A+A/A genotypes of rs12654812 had a significantly increased nephrolithiasis risk after adjusting age, sex, BMI, smoking, drinking, and hypertension, compared with G/G genotype (OR = 1.361, 95% CI = 1.033-1.794, P = .029). This hazardous effect was more pronounced in subgroup of age < 50, ever smoking, ever drinking, creatinine normal, and high uric acid. The G/A genotype of rs12654812 also had a significantly increased nephrolithiasis risk compared with G/G genotype. The A allele of rs12654812 significantly increased the risk of nephrolithiasis compared with the G allele after adjusting for age, sex, BMI, smoking, drinking and hypertension (OR = 1.277, 95% CI = 1.013-1.609, P = .038). Our results suggest that the RGS14 polymorphism is involved in the etiology of nephrolithiasis and thus may be a genetic marker for nephrolithiasis. © 2018 Wiley Periodicals, Inc.

  3. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

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    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  4. Genetic Diversity and Phylogenetic Relationships of Cytochrome C Oxidase Subunit I in Cimex hemipterus (Hemiptera: Cimicidae) Populations in Malaysia.

    Science.gov (United States)

    Seri Masran, Siti Nor Ain; Ab Majid, Abdul Hafiz

    2017-07-01

    The tropical bed bug is scientifically recognized as a significant public health problem. While there is an increased awareness about their resurgence by medical and life science committees, efficient bed bug management still remains unresolved. The solution may soon arise, as information about bed bugs' infestation dynamics and systematics are becoming more distinguishable. Recent developments in studies about bed bugs are based on molecular intervention by determining their genetic variation and phylogeography. The aim of this study is to assess the phylogenetic relationships and genetic diversity among the populations of tropical bed bugs inhabiting Malaysia. A molecular genotyping study was conducted with 22 tropical bed bug populations composed of three individuals per population. The mitochondrial (COI) gene was used as a marker. The data obtained were analyzed using the T-Coffee, ClustalX, MEGA 6.0, and PAUP software. The results showed one main monophyletic clade that consisted of two groups: Ch01 and Ch02. Ch02 consists of samples from the Bandar Hilir population, differing from the other populations studied by one singleton base. However, as there were no changes in the amino acid, this singleton genetic variation was considered to have no effect on genetic differentiation. Ch01 shows similarity with some sequence of Cimex hemipterus (F.) from Thailand, suggesting an international diversity connection. The disparity index apparently suggests that all isolates are homogeneous populations and are supported by the low value of the mean pairwise distance between isolates. This study will increase the knowledge about phylogeographic diversity of tropical bed bug in Malaysia. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Population Density Modeling for Diverse Land Use Classes: Creating a National Dasymetric Worker Population Model

    Science.gov (United States)

    Trombley, N.; Weber, E.; Moehl, J.

    2017-12-01

    Many studies invoke dasymetric mapping to make more accurate depictions of population distribution by spatially restricting populations to inhabited/inhabitable portions of observational units (e.g., census blocks) and/or by varying population density among different land classes. LandScan USA uses this approach by restricting particular population components (such as residents or workers) to building area detected from remotely sensed imagery, but also goes a step further by classifying each cell of building area in accordance with ancillary land use information from national parcel data (CoreLogic, Inc.'s ParcelPoint database). Modeling population density according to land use is critical. For instance, office buildings would have a higher density of workers than warehouses even though the latter would likely have more cells of detection. This paper presents a modeling approach by which different land uses are assigned different densities to more accurately distribute populations within them. For parts of the country where the parcel data is insufficient, an alternate methodology is developed that uses National Land Cover Database (NLCD) data to define the land use type of building detection. Furthermore, LiDAR data is incorporated for many of the largest cities across the US, allowing the independent variables to be updated from two-dimensional building detection area to total building floor space. In the end, four different regression models are created to explain the effect of different land uses on worker distribution: A two-dimensional model using land use types from the parcel data A three-dimensional model using land use types from the parcel data A two-dimensional model using land use types from the NLCD data, and A three-dimensional model using land use types from the NLCD data. By and large, the resultant coefficients followed intuition, but importantly allow the relationships between different land uses to be quantified. For instance, in the model

  6. Population structure, genetic diversity and downy mildew resistance among Ocimum species germplasm.

    Science.gov (United States)

    Pyne, Robert M; Honig, Josh A; Vaiciunas, Jennifer; Wyenandt, Christian A; Simon, James E

    2018-04-23

    The basil (Ocimum spp.) genus maintains a rich diversity of phenotypes and aromatic volatiles through natural and artificial outcrossing. Characterization of population structure and genetic diversity among a representative sample of this genus is severely lacking. Absence of such information has slowed breeding efforts and the development of sweet basil (Ocimum basilicum L.) with resistance to the worldwide downy mildew epidemic, caused by the obligate oomycete Peronospora belbahrii. In an effort to improve classification of relationships 20 EST-SSR markers with species-level transferability were developed and used to resolve relationships among a diverse panel of 180 Ocimum spp. accessions with varying response to downy mildew. Results obtained from nested Bayesian model-based clustering, analysis of molecular variance and unweighted pair group method using arithmetic average (UPGMA) analyses were synergized to provide an updated phylogeny of the Ocimum genus. Three (major) and seven (sub) population (cluster) models were identified and well-supported (P UPGMA analysis provided best resolution for the 36-accession, DM resistant k3 cluster with consistently strong bootstrap support. Although the k3 cluster is a rich source of DM resistance introgression of resistance into the commercially important k1 accessions is impeded by reproductive barriers as demonstrated by multiple sterile F1 hybrids. The k2 cluster located between k1 and k3, represents a source of transferrable tolerance evidenced by fertile backcross progeny. The 90-accession k1 cluster was largely susceptible to downy mildew with accession 'MRI' representing the only source of DM resistance. High levels of genetic diversity support the observed phenotypic diversity among Ocimum spp. accessions. EST-SSRs provided a robust evaluation of molecular diversity and can be used for additional studies to increase resolution of genetic relationships in the Ocimum genus. Elucidation of population structure

  7. Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

    Science.gov (United States)

    Maslov, Sergei; Sneppen, Kim

    2017-01-01

    Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127

  8. Increase in density of genetically diverse invasive Asian shore crab (Hemigrapsus sanguineus) populations in the Gulf of Maine.

    Science.gov (United States)

    Lord, Joshua P; Williams, Larissa M

    2017-04-01

    Hemigrapsus sanguineus , the Asian shore crab, has rapidly replaced Carcinus maenas , the green crab, as the most abundant crab on rocky shores in the northwest Atlantic since its introduction to the United States (USA) in 1988. The northern edge of this progressing invasion is the Gulf of Maine, where Asian shore crabs are only abundant in the south. We compared H. sanguineus population densities to those from published 2005 surveys and quantified genetic variation using the cytochrome c oxidase subunit I gene. We found that the range of H. sanguineus had extended northward since 2005, that population density had increased substantially (at least 10-fold at all sites), and that Asian shore crabs had become the dominant intertidal crab species in New Hampshire and southern Maine. Despite the significant increase in population density of H. sanguineus , populations only increased by a factor of 14 in Maine compared to 70 in southern New England, possibly due to cooler temperatures in the Gulf of Maine. Genetically, populations were predominantly composed of a single haplotype of Japanese, Korean, or Taiwanese origin, although an additional seven haplotypes were found. Six of these haplotypes were of Asian origin, while two are newly described. Large increases in population sizes of genetically diverse individuals in Maine will likely have a large ecological impact, causing a reduction in populations of mussels, barnacles, snails, and other crabs, similar to what has occurred at southern sites with large populations of this invasive crab species.

  9. Genetic diversity of the golden potato cyst nematode Globodera rostochiensis and determination of the origin of populations in Quebec, Canada.

    Science.gov (United States)

    Boucher, Annie Christine; Mimee, Benjamin; Montarry, Josselin; Bardou-Valette, Sylvie; Bélair, Guy; Moffett, Peter; Grenier, Eric

    2013-10-01

    The golden cyst nematode (Globodera rostochiensis), native to South America, has been introduced in many parts of the world, including Europe and North America. Recently, it was found for the first time in the province of Quebec, Canada in the locality of St. Amable near Montreal. To date, very few studies have examined the population genetics of this pest. Consequently, there is a lack of knowledge about the genetic structure and evolution of this nematode. In this study, twelve new microsatellite markers were developed in order to explore these questions. These markers were used to genotype fifteen populations originating from different regions of the world, including five from Canada. Within populations, the highest genetic diversity was consistently observed in the populations from Bolivia, the postulated region of origin of the golden nematode, and the lowest in populations from British Columbia (Canada) and New York (USA). The two Quebec populations were very similar to each other and to the population found in Newfoundland, but surprisingly, they were significantly different from three other North American populations including those from New York and British Columbia. Based on our results, we conclude that the golden cyst nematode has been introduced in North America at least twice from distinct regions of the world. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

  10. Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

    Science.gov (United States)

    Picard, Christine; Bosco, Marco

    2008-01-01

    Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

  11. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    Science.gov (United States)

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  12. MONITORING OF GENETIC DIVERSITY IN FARMED DEER POPULATIONS USING MICROSATELLITE MARKERS

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    Pavol Bajzík

    2011-12-01

    Full Text Available Deer (Cervidaei belong to the most important species used as farmed animals. We focused on assesing the genetic diversity among five deer populations. Analysis has been performed on a total of 183 animals originating from Czech Republic, Hungary, New Zealand, Poland and Slovak Republic. Genetic variability were investigated using 8 microsatellite markers used in deer. Statistical data of all populations we obtained on the basis of Nei statistics, using by POWERMARKER 3.23 programme. Graphical view of relationships among populations and individuals in the populations was obtained using the Dendroscope software. Molecular genetic data combinated with evaluation in statistical programmes could lead to a complex view of populations and diffrences among them.doi:10.5219/172

  13. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino

    2003-01-01

    conditions, but exclude factors such as animal behaviour, environmental structure, and breeding biology, all of which influence genetic diversity. Most populations are unique in some of these characteristics, and therefore may be unsuitable for the classical approach. Here, an alternative approach using...... to habitat availability and their influence on vole behaviour. Interaction between spatial and temporal dynamics altered the ratio of effective population size to census size. This indicates an altered reproductive potential, crucial in conservation biology applications. However, when the loss......Altering environmental conditions affects the genetic composition of populations via demographic and selective responses by creating of variety of population substructuring types. Classical genetic approaches can predict the genetic composition of populations under long-term or structurally stable...

  14. Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

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    A. A. Maw

    2015-01-01

    Full Text Available The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels markers. Most of the indels loci were polymorphic (71% to 96%, and the genetic variability was similar in all populations. The average observed heterozygosities (HO and expected heterozygosities (HE ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088 than Myanmar (0.041 and Laotian (0.024 populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3 from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

  15. Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China.

    Science.gov (United States)

    Zhao, Liangjie; Chenoweth, Erica L; Liu, Qigen

    2018-03-01

    In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F ST , gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

  16. Population genetic analysis of a medicinally significant Australian rainforest tree, Fontainea picrosperma C.T. White (Euphorbiaceae): biogeographic patterns and implications for species domestication and plantation establishment.

    Science.gov (United States)

    Lamont, R W; Conroy, G C; Reddell, P; Ogbourne, S M

    2016-02-29

    Fontainea picrosperma, a subcanopy tree endemic to the rainforests of northeastern Australia, is of medicinal significance following the discovery of the novel anti-cancer natural product, EBC-46. Laboratory synthesis of EBC-46 is unlikely to be commercially feasible and consequently production of the molecule is via isolation from F. picrosperma grown in plantations. Successful domestication and plantation production requires an intimate knowledge of a taxon's life-history attributes and genetic architecture, not only to ensure the maximum capture of genetic diversity from wild source populations, but also to minimise the risk of a detrimental loss in genetic diversity via founder effects during subsequent breeding programs designed to enhance commercially significant agronomic traits. Here we report the use of eleven microsatellite loci (PIC = 0.429; P ID  = 1.72 × 10(-6)) to investigate the partitioning of genetic diversity within and among seven natural populations of F. picrosperma. Genetic variation among individuals and within populations was found to be relatively low (A = 2.831; H E  = 0.407), although there was marked differentiation among populations (PhiPT = 0.248). Bayesian, UPGMA and principal coordinates analyses detected three main genotypic clusters (K = 3), which were present at all seven populations. Despite low levels of historical gene flow (N m  = 1.382), inbreeding was negligible (F = -0.003); presumably due to the taxon's dioecious breeding system. The data suggests that F. picrosperma was previously more continuously distributed, but that rainforest contraction and expansion in response to glacial-interglacial cycles, together with significant anthropogenic effects have resulted in significant fragmentation. This research provides important tools to support plantation establishment, selection and genetic improvement of this medicinally significant Australian rainforest species.

  17. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

    KAUST Repository

    Pailles, Yveline

    2017-02-15

    Endemic flora of the Galapagos Islands has adapted to thrive in harsh environmental conditions. The wild tomato species from the Galapagos Islands, Solanum cheesmaniae and S. galapagense, are tolerant to various stresses, and can be crossed with cultivated tomato. However, information about genetic diversity and relationships within and between populations is necessary to use these resources efficiently in plant breeding. In this study, we analyzed 3,974 polymorphic SNP markers, obtained through the genotyping-by-sequencing technique, DArTseq, to elucidate the genetic diversity and population structure of 67 accessions of Galapagos tomatoes (compared to two S. lycopersicum varieties and one S. pimpinellifolium accession). Two clustering methods, Principal Component Analysis and STRUCTURE, showed clear distinction between the two species and a subdivision in the S. cheesmaniae group corresponding to geographical origin and age of the islands. High genetic variation among the accessions within each species was suggested by the AMOVA. High diversity in the S. cheesmaniae group and its correlation with the islands of origin were also suggested. This indicates a possible influence of the movement of the islands, from west to east, on the gene flow. Additionally, the absence of S. galapagense populations in the eastern islands points to the species divergence occurring after the eastern islands became isolated. Based on these results, it can be concluded that the population structure of the Galapagos tomatoes collection partially explains the evolutionary history of both species, knowledge that facilitates exploitation of their genetic potential for the identification of novel alleles contributing to stress tolerance.

  18. Characterisation of adaptive genetic diversity in environmentally contrasted populations of Eucalyptus camaldulensis Dehnh. (river red gum.

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    Shannon Dillon

    Full Text Available As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh. is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST = 17%, exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2 which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.

  19. Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

    Science.gov (United States)

    Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

    2002-02-01

    Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

  20. Assessment of Genetic Diversity in Opuntia spp. Portuguese Populations Using SSR Molecular Markers

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    Carlos M. G. Reis

    2018-04-01

    Full Text Available The Opuntia spp., most likely few individuals, were introduced in the Iberian Peninsula in the beginning of the 16th century, after the discovery of America, spreading afterwards throughout the Mediterranean basin. We analysed, for the first time, the genetic diversity in a set of 19 Portuguese Opuntia spp. populations from the species O. ficus-indica, O. elata, O. dillenii and O. robusta using nuclear microsatellite (nuSSR markers. The Italian cultivars ‘Bianca’, ‘Gialla’ and ‘Rossa’ were included in the study for comparison purposes. The nuSSR amplifications produced from five to 16 alleles, with an average of 9.2 alleles per primer pair, and average polymorphism information content of 0.71. The estimated Dice coefficient among populations varied from 0.26 to 1.0, indicating high interspecific genetic diversity but low genetic diversity at the intraspecific level. The hierarchical clustering analysis revealed four major groups that clearly separated the four Opuntia species. Among the O. ficus-indica populations, two sub-clusters were found, one including the white pulp fruits (with cv. Bianca and the other with the orange pulp ones and including the cv. Gialla, the cv. Rossa, and one pale yellow pulp population. No genetic differences were found between the inermis form, O. ficus-indica f. ficus-indica, and the rewilded spiny one, O. ficus-indica f. amyclaea. The dendrogram indicated that the clustering pattern was unrelated to geographical origin. The results revealed a low level of genetic diversity among the Portuguese populations of O. ficus-indica.

  1. Ayurgenomics for stratified medicine: TRISUTRA consortium initiative across ethnically and geographically diverse Indian populations.

    Science.gov (United States)

    Prasher, Bhavana; Varma, Binuja; Kumar, Arvind; Khuntia, Bharat Krushna; Pandey, Rajesh; Narang, Ankita; Tiwari, Pradeep; Kutum, Rintu; Guin, Debleena; Kukreti, Ritushree; Dash, Debasis; Mukerji, Mitali

    2017-02-02

    Genetic differences in the target proteins, metabolizing enzymes and transporters that contribute to inter-individual differences in drug response are not integrated in contemporary drug development programs. Ayurveda, that has propelled many drug discovery programs albeit for the search of new chemical entities incorporates inter-individual variability "Prakriti" in development and administration of drug in an individualized manner. Prakriti of an individual largely determines responsiveness to external environment including drugs as well as susceptibility to diseases. Prakriti has also been shown to have molecular and genomic correlates. We highlight how integration of Prakriti concepts can augment the efficiency of drug discovery and development programs through a unique initiative of Ayurgenomics TRISUTRA consortium. Five aspects that have been carried out are (1) analysis of variability in FDA approved pharmacogenomics genes/SNPs in exomes of 72 healthy individuals including predominant Prakriti types and matched controls from a North Indian Indo-European cohort (2) establishment of a consortium network and development of five genetically homogeneous cohorts from diverse ethnic and geo-climatic background (3) identification of parameters and development of uniform standard protocols for objective assessment of Prakriti types (4) development of protocols for Prakriti evaluation and its application in more than 7500 individuals in the five cohorts (5) Development of data and sample repository and integrative omics pipelines for identification of genomic correlates. Highlight of the study are (1) Exome sequencing revealed significant differences between Prakriti types in 28 SNPs of 11 FDA approved genes of pharmacogenomics relevance viz. CYP2C19, CYP2B6, ESR1, F2, PGR, HLA-B, HLA-DQA1, HLA-DRB1, LDLR, CFTR, CPS1. These variations are polymorphic in diverse Indian and world populations included in 1000 genomes project. (2) Based on the phenotypic attributes of

  2. Estimates of population genetic diversity in brown bullhead catfish by DNA fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Roth, A.C.; Wessendarp, T.K.; Gordon, D.A.; Smith, M.K. [Environmental Protection Agency, Cincinnati, OH (United States); Lattier, D.L. [Oak Ridge Inst. for Science and Education, Cincinnati, OH (United States); Hertzberg, V.; Leonard, A. [Univ. of Cincinnati, OH (United States). Dept. of Environmental Health

    1994-12-31

    Estimates of population genetic diversity may be a sensitive indicator of environmental impact, since limiting the effective breeding population by any means will result in loss of some variant genotypes, as has been demonstrated by allozyme analysis. DNA fingerprinting techniques are also coming into use for population analyses, and the authors chose to apply fingerprinting analysis three populations of brown bullhead catfish collected in Northern Ohio. DNA was isolated from the red blood cells of individual fish. Purified DNAs were digested with EcoR1 restriction enzyme; the digests were then sized on a 1% agarose gel, transferred to nylon membranes and probed with a radiolabeled M13 probe using the Westneat hybridization protocol (Southern blotting). This method effects fragments containing VNTR (variable number of tandem repeat) sequences complementary to the M13, which are highly variable among individual catfish. Hybridized bands were visualized by a Molecular Dynamics phosphorimager and recorded and analyzed with its proprietary Imagequant image analysis program, Excel and SAS. A total of 10 variable bands were identified and their presence or absence scored in each individual. These data were analyzed to determine between and within-population similarity indices as well as population heterozygosity and genetic diversity measures.

  3. Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

    Directory of Open Access Journals (Sweden)

    Bianca W. Bertoni

    2010-01-01

    Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

  4. A normative study of lexical verbal fluency in an educationally-diverse elderly population.

    Science.gov (United States)

    Kim, Bong Jo; Lee, Cheol Soon; Oh, Byoung Hoon; Hong, Chang Hyung; Lee, Kang Soo; Son, Sang Joon; Han, Changsu; Park, Moon Ho; Jeong, Hyun-Ghang; Kim, Tae Hui; Park, Joon Hyuk; Kim, Ki Woong

    2013-12-01

    Lexical fluency tests are frequently used to assess language and executive function in clinical practice. We investigated the influences of age, gender, and education on lexical verbal fluency in an educationally-diverse, elderly Korean population and provided its' normative information. We administered the lexical verbal fluency test (LVFT) to 1676 community-dwelling, cognitively normal subjects aged 60 years or over. In a stepwise linear regression analysis, education (B=0.40, SE=0.02, standardized B=0.506) and age (B=-0.10, SE=0.01, standardized B=-0.15) had significant effects on LVFT scores (p0.05). Education explained 28.5% of the total variance in LVFT scores, which was much larger than the variance explained by age (5.42%). Accordingly, we presented normative data of the LVFT stratified by age (60-69, 70-74, 75-79, and ≥80 years) and education (0-3, 4-6, 7-9, 10-12, and ≥13 years). The LVFT norms should provide clinically useful data for evaluating elderly people and help improve the interpretation of verbal fluency tasks and allow for greater diagnostic accuracy.

  5. Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.

    Science.gov (United States)

    Zhang, Xiao; Zhang, Hua; Li, Lujiang; Lan, Hai; Ren, Zhiyong; Liu, Dan; Wu, Ling; Liu, Hailan; Jaqueth, Jennifer; Li, Bailin; Pan, Guangtang; Gao, Shibin

    2016-08-31

    Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs). With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5-3 Mb) than that in the entire panel (0.5-0.75 Mb) and the Tropical group (0.25-0.5 Mb). A large region at 30-120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines. For the panel covered most of widely used inbred lines in Southwest China, this work

  6. Significant association of SREBP-2 genetic polymorphisms with avascular necrosis in the Korean population

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    Park Eui

    2008-10-01

    Full Text Available Abstract Background It is known that steroid usage and alcohol abuse are major etiological factors in the development of avascular necrosis (AVN, a bone disease that produces osteonecrosis of the femoral head. The facilitation of fat biosynthesis by steroids and alcohol disrupts the blood supply into the femoral head. SREBP-2 plays a central role in the maintenance of lipid homeostasis through stimulating expression of genes associated with cholesterol biosynthetic pathways. The aim of this study was to examine the association between the polymorphisms of the SREBP-2 gene and AVN susceptibility in the Korean population. Methods Four single nucleotide polymorphisms (SNP in the SREBP-2 gene, IVS1+8408 T>C (rs2267439, IVS3-342 G>T (rs2269657, IVS11+414 G>A (rs1052717 and IVS12-1667 G>A (rs2267443, were selected from public databases and genotyped in 443 AVN patients and 273 control subjects by using single-based extension (SBE genotyping. Results The minor allele (C frequency of rs2267439 showed a significant protective effect on AVN (P = 0.01, OR; 0.75, 95% CI; 0.604–0.935, and the genotype frequencies of this polymorphism were also different from the controls in all alternative analysis models (P range, 0.009–0.03, OR; 0.647–0.744. In contrast, rs1052717 and rs2267443 polymorphisms were significantly associated with AVN risk. Further analysis based on pathological etiology showed that the genotypes of rs2267439, rs1052717 and rs2267443 were also significantly associated with AVN susceptibility in each subgroup. Conclusion This study is the first report to evaluate the association between SREBP-2 gene polymorphisms and the susceptibility of AVN in the Korean population.

  7. Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

    Science.gov (United States)

    Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

    2015-08-01

    The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove

  8. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

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    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  9. Blood Groups Distribution and Gene Diversity of the ABO and Rh (D Loci in the Mexican Population

    Directory of Open Access Journals (Sweden)

    Adrián Canizalez-Román

    2018-01-01

    Full Text Available Objective. To determine the frequency and distribution of ABO and Rh (D antigens and, additionally, investigate gene diversity and the structure of Mexican populations. Materials and Methods. Blood groups were tested in 271,164 subjects from 2014 to 2016. The ABO blood group was determined by agglutination using the antibodies anti-A, Anti-B, and Anti-D for the Rh factor, respectively. Results. The overall distribution of ABO and Rh (D groups in the population studied was as follows: O: 61.82%; A: 27.44%; B: 8.93%; and AB: 1.81%. For the Rh group, 95.58% of people were Rh (D, and 4.42% were Rh (d. Different distributions of blood groups across regions were found; additionally, genetic analysis revealed that the IO and ID allele showed an increasing trend from the north to the center, while the IA and Id allele tended to increase from the center to the north. Also, we found more gene diversity in both loci in the north compared with the center, suggesting population structure in Mexico. Conclusion. This work could help health institutions to identify where they can obtain blood products necessary for medical interventions. Moreover, this piece of information contributes to the knowledge of the genetic structure of the Mexican populations which could have significant implications in different fields of biomedicine.

  10. Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae: Culex spp. from the Sonoran Desert of North America

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    Edward Pfeiler

    2013-01-01

    Full Text Available The population genetics and phylogenetic relationships of Culex mosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochrome c oxidase subunit I (COI from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding to Cx. quinquefasciatus, Cx. tarsalis, and two unidentified species, Culex sp. 1 and sp. 2. Culex quinquefasciatus was found at all localities and was the most abundant species collected. Culex tarsalis was collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species of Culex were most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower in Cx. quinquefasciatus compared with the other three species. Analysis of molecular variance revealed little structure among seven populations of Cx. quinquefasciatus, whereas significant structure was found between the two populations of Cx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found for Cx. tarsalis. Possible explanations for the large differences in genetic diversity between Cx. quinquefasciatus and the other species of Culex are presented.

  11. A genetically diverse but distinct North American population of Sarcocystis neurona includes an overrepresented clone described by 12 microsatellite alleles.

    Science.gov (United States)

    Asmundsson, Ingrid M; Dubey, J P; Rosenthal, Benjamin M

    2006-09-01

    The population genetics and systematics of most coccidians remain poorly defined despite their impact on human and veterinary health. Non-recombinant parasite clones characterized by distinct transmission and pathogenesis traits persist in the coccidian Toxoplasma gondii despite opportunities for sexual recombination. In order to determine whether this may be generally true for tissue-cyst forming coccidia, and to address evolutionary and taxonomic problems within the genus Sarcocystis, we characterized polymorphic microsatellite markers in Sarcocystis neurona, the major causative agent of equine protozoal myeloencephalitis (EPM). Bayesian statistical modeling, phylogenetic reconstruction based on genotypic chord distances, and analyses of linkage disequilibrium were employed to examine the population structure within S. neurona and closely related Sarcocystis falcatula isolates from North and South America. North American S. neurona were clearly differentiated from those of South America and also from isolates of S. falcatula. Although S. neurona is characterized by substantial allelic and genotypic diversity typical of interbreeding populations, one genotype occurs with significantly excessive frequency; thus, some degree of asexual propagation of S. neurona clones may naturally occur. Finally, S. neurona isolated from disparate North American localities and diverse hosts (opossums, a Southern sea otter, and horses) comprise a single genetic population. Isolates associated with clinical neurological disease bear no obvious distinction as measured by these presumably neutral genetic markers.

  12. Autosomal genetic diversity in non-breed horses from eastern Eurasia provides insights into historical population movements.

    Science.gov (United States)

    Warmuth, Vera; Manica, Andrea; Eriksson, Anders; Barker, Graeme; Bower, Mim

    2013-02-01

    Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within- and between-population genetic diversity in 'non-breed horses' (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non-breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F (ST) was very low (range: <0.001 to -0.033), suggesting historically high levels of gene flow. Our analyses of non-breed horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  13. Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae: Culex spp.) from the Sonoran Desert of North America

    Science.gov (United States)

    Pfeiler, Edward; Flores-López, Carlos A.; Mada-Vélez, Jesús Gerardo; Escalante-Verdugo, Juan; Markow, Therese A.

    2013-01-01

    The population genetics and phylogenetic relationships of Culex mosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding to Cx. quinquefasciatus, Cx. tarsalis, and two unidentified species, Culex sp. 1 and sp. 2. Culex quinquefasciatus was found at all localities and was the most abundant species collected. Culex tarsalis was collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species of Culex were most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower in Cx. quinquefasciatus compared with the other three species. Analysis of molecular variance revealed little structure among seven populations of Cx. quinquefasciatus, whereas significant structure was found between the two populations of Cx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found for Cx. tarsalis. Possible explanations for the large differences in genetic diversity between Cx. quinquefasciatus and the other species of Culex are presented. PMID:24302868

  14. Genetic diversity and population structure of the New World screwworm fly from the Amazon region of Brazil.

    Science.gov (United States)

    Mastrangelo, Thiago; Fresia, Pablo; Lyra, Mariana L; Rodrigues, Rosangela A; Azeredo-Espin, Ana Maria L

    2014-10-01

    Cochliomyia hominivorax (Coquerel) is a myiasis fly that causes economic losses to livestock farmers in warmer American regions. Previous studies of this pest had found population structure at north and south of the Amazon Basin, which was considered to be a barrier to dispersal. The present study analyzed three mitochondrial DNA (mtDNA) markers and eight nuclear microsatellite loci to investigate for the first time the genetic diversity and population structure across the Brazilian Amazon region (Amazonia). Both mtDNA and microsatellite data supported the existence of much diversity and significant population structure among nine regional populations of C. hominivorax, which was found to be surprisingly common in Amazonia. Forty-six mtDNA haplotypes were identified, of which 39 were novel and seven had previously been found only at south of Amazonia. Seventy microsatellite alleles were identified by size, moderate to high values of heterozygosity were discovered in all regions, and a Bayesian clustering analysis identified four genetic groups that were not geographically distributed. Reproductive compatibility was also investigated by laboratory crossing, but no evidence of hybrid dysgenesis was found between an Amazonian colony and one each of from Northeast and Southeast Brazil. The results have important implications for area-wide control by the Sterile Insect Technique. Copyright © 2014 International Atomic Energy Agency 2014. Published by Elsevier B.V. All rights reserved.

  15. The Genetic Diversity and Structure of Linkage Disequilibrium of the MTHFR Gene in Populations of Northern Eurasia.

    Science.gov (United States)

    Trifonova, E A; Eremina, E R; Urnov, F D; Stepanov, V A

    2012-01-01

    The structure of the haplotypes and linkage disequilibrium (LD) of the methylenetetrahydrofolate reductase gene (MTHFR) in 9 population groups from Northern Eurasia and populations of the international HapMap project was investigated in the present study. The data suggest that the architecture of LD in the human genome is largely determined by the evolutionary history of populations; however, the results of phylogenetic and haplotype analyses seems to suggest that in fact there may be a common "old" mechanism for the formation of certain patterns of LD. Variability in the structure of LD and the level of diversity of MTHFRhaplotypes cause a certain set of tagSNPs with an established prognostic significance for each population. In our opinion, the results obtained in the present study are of considerable interest for understanding multiple genetic phenomena: namely, the association of interpopulation differences in the patterns of LD with structures possessing a genetic susceptibility to complex diseases, and the functional significance of the pleiotropicMTHFR gene effect. Summarizing the results of this study, a conclusion can be made that the genetic variability analysis with emphasis on the structure of LD in human populations is a powerful tool that can make a significant contribution to such areas of biomedical science as human evolutionary biology, functional genomics, genetics of complex diseases, and pharmacogenomics.

  16. LOD significance thresholds for QTL analysis in experimental populations of diploid species

    Science.gov (United States)

    Van Ooijen JW

    1999-11-01

    Linkage analysis with molecular genetic markers is a very powerful tool in the biological research of quantitative traits. The lack of an easy way to know what areas of the genome can be designated as statistically significant for containing a gene affecting the quantitative trait of interest hampers the important prediction of the rate of false positives. In this paper four tables, obtained by large-scale simulations, are presented that can be used with a simple formula to get the false-positives rate for analyses of the standard types of experimental populations with diploid species with any size of genome. A new definition of the term 'suggestive linkage' is proposed that allows a more objective comparison of results across species.

  17. Population genetic diversity and structure analysis of wild apricot (Prunus armeniaca L.) revealed by ssr markers in the Tien-Shan mountains of China

    International Nuclear Information System (INIS)

    Hu, X.; Ni, B.; Zheng, P.; Li, M.

    2018-01-01

    The simple sequence repeat markers were used to investigate the population genetic diversity and structure of 212 germplasm samples from 14 apricot (Prunus armeniaca) populations in the western of Tien-Shan Mountains, Sinkiang, China. The relatively high expected heterozygosity and Shannon's diversity index indicated the apricot populations maintained a high level of genetic diversity (He = 0.6109, I = 1.2208), with the population in Tuergen ditch of Xinyuan County having the highest genetic diversity index. A high level of intra-population genetic differentiation (91.51%) and a lower level of inter-population genetic differentiation were occurred, as well as a moderate but steady inter-population gene flow (Nm = 2.3735). The self-incompatible pattern, wide distribution, and long-distance pollen transmission via insects and gale are the main factors underlying the genetic variation structure. The UPGMA cluster analysis and genetic structure analysis showed that apricot germplasm could be divided into two or four groups, which was basically consistent with the geographic distribution pattern. The inter-population genetic distance and geographic distance showed a significant correlation (r = 0.2658, p<0.05). (author)

  18. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

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    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  19. Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant.

    Science.gov (United States)

    Rabeling, Christian; Gonzales, Omar; Schultz, Ted R; Bacci, Maurício; Garcia, Marcos V B; Verhaagh, Manfred; Ishak, Heather D; Mueller, Ulrich G

    2011-07-26

    Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species Mycocepurus smithii was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless, M. smithii is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that M. smithii actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in M. smithii. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that M. smithii is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that M. smithii evolved 0.5-1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.

  20. Molecular Markers for Genetic Diversity Studies of European Hare (Lepus europaeus Pallas, 1778 Populations

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    Noémi Soós

    2015-05-01

    Full Text Available The purpose of this article is to give an overview of different molecular techniques which have been used in studies concerning population genetic issues of Lepus species and specifically of L. europaeus. The importance of these researches is ever-growing as the European populations of the brown hare have suffered several falloffs as a consequent upon both natural and anthropogenic effects. With developing tools and techniques molecular genetics have become the centrepiece of population genetics and conservation biology. Nucleic acid methods based on both bi- and uniparentally inherited DNA (allozymes, microsatellites, Y chromosome, mtDNA are often used to study genetic structure, diversity and phylogeography of different species’ populations due to their effectiveness in identifying genetic variability

  1. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.

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    Ganal Martin W

    2006-01-01

    Full Text Available Abstract Background The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles, Principal Coordinate Analysis (PCoA, and analysis of genome-wide linkage disequilibrium. Results A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i geographical regions and (ii agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD was estimated as squared correlation of allele frequencies (r2. The values of LD for barley were comparable to other plant species (conifers, poplar, maize. The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P 0.80 provided higher LD values as compared to 19 low polymorphic loci (PIC Conclusion A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing

  2. Genetic diversity and relatedness among seven red deer (Cervus elaphus populations

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    Lenka Maršálková

    2014-02-01

    Full Text Available Deer (Cervidae recently belongs to the most important species. The aim of presenting study was evaluation of genetic diversity and relationship within and among seven red deer populations from different origins - Czech Republic, Hungary, hybrids Hungary x New Zealand, Lithuania, New Zealand, Poland and Slovak Republic. This study was conducted to determine the levels of genetic variability and relationships among deer populations from a total of 637 animals originating from seven countries Czech Republic (50, Hungary (35, Hungary x New Zealand hybrids (67, Lithuania (26, New Zealand (82, Poland (347 and Slovak Republic (30.  We used the hair bulbs as a source of DNA.  In total, 213 alleles were observed from the 10 loci surveyed. The number of alleles per locus ranged from 11 (IOBT965 to 35 (T156, RT13. Genetic diversity and relatedness among red deer populations has been performed on a total of 637 animals. A panel of 10 microsatellite markers used in deer were optimized. On the basis of this panel of microsatellites we were investigated genetic variability and relationships by using statistical and graphical programmes. We evaluated how close populations are to each other and their genetic admixture. Molecular genetic data combined with evaluation in statistical programmes could lead to a complex view of populations

  3. Giving Context to the Physician Competency Reference Set: Adapting to the Needs of Diverse Populations

    Science.gov (United States)

    Eckstrand, Kristen L.; Potter, Jennifer; Bayer, Carey Roth; Englander, Robert

    2016-01-01

    Delineating the requisite competencies of a 21st-century physician is the first step in the paradigm shift to competency-based medical education. Over the past two decades, more than 150 lists of competencies have emerged. In a synthesis of these lists, the Physician Competency Reference Set (PCRS) provided a unifying framework of competencies that define the general physician. The PCRS is not context or population specific; however, competently caring for certain underrepresented populations or specific medical conditions can require more specific context. Previously developed competency lists describing care for these populations have been disconnected from an overarching competency framework, limiting their uptake. To address this gap, the Association of American Medical Colleges Advisory Committee on Sexual Orientation, Gender Identity, and Sex Development adapted the PCRS by adding context- and content-specific qualifying statements to existing PCRS competencies to better meet the needs of diverse patient populations. This Article describes the committee’s process in developing these qualifiers of competence. To facilitate widespread adoption of the contextualized competencies in U.S. medical schools, the committee used an established competency framework to develop qualifiers of competence to improve the health of individuals who are lesbian, gay, bisexual, transgender; gender nonconforming; or born with differences in sexual development. This process can be applied to other underrepresented populations or medical conditions, ensuring that relevant topics are included in medical education and, ultimately, health care outcomes are improved for all patients inclusive of diversity, background, and ability. PMID:26796092

  4. RAPD markers on genetic diversity in three populations of pisifera type of oil palm (elaeis guineensis)

    Science.gov (United States)

    Basyuni, M.; Prayogi, H.; Putri, L. A. P.; Syahputra, I.; Siregar, E. S.; Risnasari, I.; Wati, R.; Arifiyanto, D.

    2018-03-01

    Palm oil (E. guineensis) is one of the major commodity and contributing largely to non-petroleum oil of Indonesian foreign exchange. E. guineensis has three fruit types, dura (female), pisifera (male), and tenera —a hybrid between dura and pisifera. Pisifera plays an important function in the production of seed oil palm. The purpose of this research is to analyze genetic diversity of pisifera type of E. guineensis from three populations, Yangambi, Lame and Lame further cross in Bangun Bandar, North Sumatra, Indonesia. Eighteen samples for each population were analyzed using six RAPD markers. Results showed that RAPD markers were low polymorphic with 1.49, 1.39, and 1.00 average number alleles detected for Yagambi, Lame, and Lame further cross, respectively. The level of genetic diversity detected for each population was 0.28, 0.22, and 0.21 for Yagambi, Lame, and Lame further cross, respectively, indicating that the populations had little genetic variation. The highest of polymorphic information content (PIC) was found on the P11 primer of Yangambi (0.49) and P10 primer for lame further cross (0.49). By contrast, the lowest PIC belongs to P21 for Lame population (0.01). This data is likely to contributing oil palm breeding.

  5. Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa in Brazil

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    Camila L. Clozato

    Full Text Available Abstract The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758 belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b and two nuclear markers (AMELY and RAG2. We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

  6. Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

    Science.gov (United States)

    Clozato, Camila L; Miranda, Flávia R; Lara-Ruiz, Paula; Collevatti, Rosane G; Santos, Fabrício R

    2017-01-01

    The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and RAG2). We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

  7. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae) on the Canary Islands.

    Science.gov (United States)

    Sun, Ye; Vargas-Mendoza, Carlos F

    2017-01-01

    Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west-east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  8. Population Structure, Genetic Diversity, and Evolutionary History of Kleinia neriifolia (Asteraceae on the Canary Islands

    Directory of Open Access Journals (Sweden)

    Ye Sun

    2017-06-01

    Full Text Available Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat. The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote and western islands (EI Hierro, La Palma, La Gomera, Tenerife, this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.

  9. Selection for silage yield and composition did not affect genomic diversity within the Wisconsin Quality Synthetic maize population.

    Science.gov (United States)

    Lorenz, Aaron J; Beissinger, Timothy M; Silva, Renato Rodrigues; de Leon, Natalia

    2015-02-02

    Maize silage is forage of high quality and yield, and represents the second most important use of maize in the United States. The Wisconsin Quality Synthetic (WQS) maize population has undergone five cycles of recurrent selection for silage yield and composition, resulting in a genetically improved population. The application of high-density molecular markers allows breeders and geneticists to identify important loci through association analysis and selection mapping, as well as to monitor changes in the distribution of genetic diversity across the genome. The objectives of this study were to identify loci controlling variation for maize silage traits through association analysis and the assessment of selection signatures and to describe changes in the genomic distribution of gene diversity through selection and genetic drift in the WQS recurrent selection program. We failed to find any significant marker-trait associations using the historical phenotypic data from WQS breeding trials combined with 17,719 high-quality, informative single nucleotide polymorphisms. Likewise, no strong genomic signatures were left by selection on silage yield and quality in the WQS despite genetic gain for these traits. These results could be due to the genetic complexity underlying these traits, or the role of selection on standing genetic variation. Variation in loss of diversity through drift was observed across the genome. Some large regions experienced much greater loss in diversity than what is expected, suggesting limited recombination combined with small populations in recurrent selection programs could easily lead to fixation of large swaths of the genome. Copyright © 2015 Lorenz et al.

  10. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    International Nuclear Information System (INIS)

    Yuhki, Naoya; O'Brien, S.J.

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations

  11. Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata L. Walp).

    Science.gov (United States)

    Xiong, Haizheng; Shi, Ainong; Mou, Beiquan; Qin, Jun; Motes, Dennis; Lu, Weiguo; Ma, Jianbing; Weng, Yuejin; Yang, Wei; Wu, Dianxing

    2016-01-01

    The genetic diversity of cowpea was analyzed, and the population structure was estimated in a diverse set of 768 cultivated cowpea genotypes from the USDA GRIN cowpea collection, originally collected from 56 countries. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the identified SNP alleles were used to estimate the level of genetic diversity, population structure, and phylogenetic relationships. The aim of this study was to detect the gene pool structure of cowpea and to determine its relationship between different regions and countries. Based on the model-based ancestry analysis, the phylogenetic tree, and the principal component analysis, three well-differentiated genetic populations were postulated from 768 worldwide cowpea genotypes. According to the phylogenetic analyses between each individual, region, and country, we may trace the accession from off-original, back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. To our knowledge, this is the first report of the analysis of the genetic variation and relationship between globally cultivated cowpea genotypes. The results will help curators, researchers, and breeders to understand, utilize, conserve, and manage the collection for more efficient contribution to international cowpea research.

  12. DNA variation of the mammalian major histocompatibility complex reflects genomic diversity and population history

    Energy Technology Data Exchange (ETDEWEB)

    Yuhki, Naoya; O' Brien, S.J. (National Cancer Institute, Frederick, MD (USA))

    1990-01-01

    The major histocompatibility complex (MHC) is a multigene complex of tightly linked homologous genes that encode cell surface antigens that play a key role in immune regulation and response to foreign antigens. In most species, MHC gene products display extreme antigenic polymorphism, and their variability has been interpreted to reflect an adaptive strategy for accommodating rapidly evolving infectious agents that periodically afflict natural populations. Determination of the extent of MHC variation has been limited to populations in which skin grafting is feasible or for which serological reagents have been developed. The authors present here a quantitative analysis of restriction fragment length polymorphism of MHC class I genes in several mammalian species (cats, rodents, humans) known to have very different levels of genetic diversity based on functional MHC assays and on allozyme surveys. When homologous class I probes were employed, a notable concordance was observed between the extent of MHC restriction fragment variation and functional MHC variation detected by skin grafts or genome-wide diversity estimated by allozyme screens. These results confirm the genetically depauperate character of the African cheetah, Acinonyx jubatus, and the Asiatic lion, Panthera leo persica; further, they support the use of class I MHC molecular reagents in estimating the extent and character of genetic diversity in natural populations.

  13. Genetic diversity and population structure of Lactobacillus delbrueckii subspecies bulgaricus isolated from naturally fermented dairy foods.

    Science.gov (United States)

    Song, Yuqin; Sun, Zhihong; Guo, Chenyi; Wu, Yarong; Liu, Wenjun; Yu, Jie; Menghe, Bilige; Yang, Ruifu; Zhang, Heping

    2016-03-04

    Lactobacillus delbrueckii subsp. bulgaricus is one of the most widely used starter culture strains in industrial fermented dairy manufacture. It is also common in naturally fermented dairy foods made using traditional methods. The subsp. bulgaricus strains found in naturally fermented foods may be useful for improving current industrial starter cultures; however, little is known regarding its genetic diversity and population structure. Here, a collection of 298 L. delbrueckii strains from naturally fermented products in Mongolia, Russia, and West China was analyzed by multi-locus sequence typing based on eight conserved genes. The 251 confirmed subsp. bulgaricus strains produced 106 unique sequence types, the majority of which were assigned to five clonal complexes (CCs). The geographical distribution of CCs was uneven, with CC1 dominated by Mongolian and Russian isolates, and CC2-CC5 isolates exclusively from Xinjiang, China. Population structure analysis suggested six lineages, L1-L6, with various homologous recombination rates. Although L2-L5 were mainly restricted within specific regions, strains belonging to L1 and L6 were observed in diverse regions, suggesting historical transmission events. These results greatly enhance our knowledge of the population diversity of subsp. bulgaricus strains, and suggest that strains from CC1 and L4 may be useful as starter strains in industrial fermentation.

  14. Geographic distribution of genetic diversity in populations of Rio Grande Chub Gila pandora

    Science.gov (United States)

    Galindo, Rene; Wilson, Wade; Caldwell, Colleen A.

    2016-01-01

    In the southwestern United States (US), the Rio Grande chub (Gila pandora) is state-listed as a fish species of greatest conservation need and federally listed as sensitive due to habitat alterations and competition with non-native fishes. Characterizing genetic diversity, genetic population structure, and effective number of breeders will assist with conservation efforts by providing a baseline of genetic metrics. Genetic relatedness within and among G. pandora populations throughout New Mexico was characterized using 11 microsatellite loci among 15 populations in three drainage basins (Rio Grande, Pecos, Canadian). Observed heterozygosity (HO) ranged from 0.71–0.87 and was similar to expected heterozygosity (0.75–0.87). Rio Ojo Caliente (Rio Grande) had the highest allelic richness (AR = 15.09), while Upper Rio Bonito (Pecos) had the lowest allelic richness (AR = 6.75). Genetic differentiation existed among all populations with the lowest genetic variation occurring within the Pecos drainage. STRUCTURE analysis revealed seven genetic clusters. Populations of G. pandora within the upper Rio Grande drainage (Rio Ojo Caliente, Rio Vallecitos, Rio Pueblo de Taos) had high levels of admixture with Q-values ranging from 0.30–0.50. In contrast, populations within the Pecos drainage (Pecos River and Upper Rio Bonito) had low levels of admixture (Q = 0.94 and 0.87, respectively). Estimates of effective number of breeders (N b ) varied from 6.1 (Pecos: Upper Rio Bonito) to 109.7 (Rio Grande: Rio Peñasco) indicating that populations in the Pecos drainage are at risk of extirpation. In the event that management actions are deemed necessary to preserve or increase genetic diversity of G. pandora, consideration must be given as to which populations are selected for translocation.

  15. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China.

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    Hailong Dou

    Full Text Available Over the past century, the endangered Amur tiger (Panthera tigris altaica has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9-11 tigers during the winter of 2014-2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

  16. Estimating the Population Size and Genetic Diversity of Amur Tigers in Northeast China.

    Science.gov (United States)

    Dou, Hailong; Yang, Haitao; Feng, Limin; Mou, Pu; Wang, Tianming; Ge, Jianping

    2016-01-01

    Over the past century, the endangered Amur tiger (Panthera tigris altaica) has experienced a severe contraction in demography and geographic range because of habitat loss, poaching, and prey depletion. In its historical home in Northeast China, there appears to be a single tiger population that includes tigers in Southwest Primorye and Northeast China; however, the current demographic status of this population is uncertain. Information on the abundance, distribution and genetic diversity of this population for assessing the efficacy of conservation interventions are scarce. We used noninvasive genetic detection data from scats, capture-recapture models and an accumulation curve method to estimate the abundance of Amur tigers in Northeast China. We identified 11 individual tigers (6 females and 5 males) using 10 microsatellite loci in three nature reserves between April 2013 and May 2015. These tigers are confined primarily to a Hunchun Nature Reserve along the border with Russia, with an estimated population abundance of 9-11 tigers during the winter of 2014-2015. They showed a low level of genetic diversity. The mean number of alleles per locus was 2.60 and expected and observed heterozygosity were 0.42 and 0.49, respectively. We also documented long-distance dispersal (~270 km) of a male Amur tiger to Huangnihe Nature Reserve from the border, suggesting that the expansion of neighboring Russian populations may eventually help sustain Chinese populations. However, the small and isolated population recorded by this study demonstrate that there is an urgent need for more intensive regional management to create a tiger-permeable landscape and increased genetic connectivity with other populations.

  17. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis as Revealed by Mitochondrial and Microsatellite DNA

    Directory of Open Access Journals (Sweden)

    Minmin Chen

    2014-06-01

    Full Text Available Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS, and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY and Tongling (TL and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP.

  18. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis) as Revealed by Mitochondrial and Microsatellite DNA

    Science.gov (United States)

    Chen, Minmin; Zheng, Jinsong; Wu, Min; Ruan, Rui; Zhao, Qingzhong; Wang, Ding

    2014-01-01

    Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis) is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA) control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS), and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY) and Tongling (TL)) and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP. PMID:24968271

  19. Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu.

    Science.gov (United States)

    Wang, Xin; Luo, Guangbin; Yang, Wenlong; Li, Yiwen; Sun, Jiazhu; Zhan, Kehui; Liu, Dongcheng; Zhang, Aimin

    2017-07-01

    Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.

  20. Concerned significant others of people with gambling problems in Finland: a cross-sectional population study.

    Science.gov (United States)

    Salonen, Anne H; Castrén, Sari; Alho, Hannu; Lahti, Tuuli

    2014-04-24

    Problem gambling not only impacts those directly involved, but also the concerned significant others (CSOs) of problem gamblers. The aims of this study were to investigate the proportion of male and female CSOs at the population level; to investigate who the CSOs were concerned about; and to investigate sociodemographic factors, gender differences, gambling behaviour, and health and well-being among CSOs and non-CSOs. The data (n = 4484) were based on a cross-sectional population study. Structured telephone interviews were conducted in 2011-2012. The data were weighted based on age, gender and residency. The respondents were defined as CSOs if they reported that at least one of their significant others (father, mother, sister/brother, grandparent, spouse, own child/children, close friend) had had gambling problems. Statistical significance was determined by chi-squared and Fisher's exact tests, and logistic regression analysis. Altogether, 19.3% of the respondents were identified as CSOs. Most commonly, the problem gambler was a close friend (12.4%) of the CSO. The percentage of close friends having a gambling problem was larger among male CSOs (14.4%) compared with female CSOs (10.3%; p ≤ 0.001), while the percentage of partners with gambling problem was larger among females (2.6%) than among males (0.8%; p ≤ 0.001). In the best fitting model, the odds ratio (95% CI) of being a male CSO was 2.03 (1.24-3.31) for past-year gambling problems, 1.46 (1.08-1.97) for loneliness and 1.78 (1.38-2.29) for risky alcohol consumption. The odds ratio (95% CI) of being a female CSO was 1.51 (1.09-2.08) for past-year gambling involvement, 3.05 (1.18-7.90) for past-year gambling problems, 2.21 (1.24-3.93) for mental health problems, 1.39 (1.03-1.89) for loneliness and 1.97 (1.43-2.71) for daily smoking. CSOs of problem gamblers often experience cumulating problems such as their own risky gambling behaviour, health problems and other addictive disorders. The

  1. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

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    Jurado Juan J

    2009-09-01

    Full Text Available Abstract Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008 consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08 mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will

  2. A reduced number of mtSNPs saturates mitochondrial DNA haplotype diversity of worldwide population groups.

    Science.gov (United States)

    Salas, Antonio; Amigo, Jorge

    2010-05-03

    The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations ("African-Americans" and "Hispanics") were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of "universal" mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to

  3. Spatial distribution of insecticide resistance in Caribbean populations of Aedes aegypti and its significance

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    Rawlins Samuel C.

    1998-01-01

    Full Text Available To monitor resistance to insecticides, bioassays were performed on 102 strains of the dengue vector Aedes aegypti (L. from 16 countries ranging from Suriname in South America and through the chain of Caribbean Islands to the Bahamas, where the larvicide temephos and the adulticide malathion have been in use for 15 to 30 years. There was wide variation in the sensitivity to the larvicide in mosquito populations within and among countries. Mosquito strains in some countries such as Antigua, St. Lucia, and Tortola had consistently high resistance ratios (RR to temephos, ranging from 5.3 to 17.7. In another group of countries-e.g., Anguilla and Curaçao-mosquitoes had mixed levels of resistance to temephos (RR = 2.5-10.6, and in a third group of countries, including St. Kitts, Barbados, Jamaica, and Suriname, mosquitoes had consistently low levels of resistance to temephos (RR = 1- 4.6 (P < 0.05. On occasion significantly different levels of resistance were recorded from neighboring A. aegypti communities, which suggests there is little genetic exchange among populations. The impact of larval resistance expressed itself as reduced efficacy of temephos to kill mosquitoes when strains were treated in the laboratory or in the field in large container environments with recommended dosages. Although a sensitive strain continued to be completely controlled for up to 7 weeks, the most resistant strains had 24% survival after the first week. By week 6, 60% to 75% of all resistant strains of larvae were surviving the larval period. Responses to malathion in adult A. aegypti varied from a sensitive population in Suriname (RR = 1.3 to resistant strains in St. Vincent (RR = 4.4, Dominica (RR = 4.2, and Trinidad (RR = 4.0; however, resistance was generally not on the scale of that observed to temephos in the larval stages and had increased only slightly when compared to the levels that existed 3 to 4 years ago. Suggestions are made for a pesticide usage policy

  4. WITHIN-POPULATION GENETIC DIVERSITY OF CLIMBING PLANTS AND TREES IN A TEMPERATE FOREST IN CENTRAL CHILE

    OpenAIRE

    Torres-Díaz, Cristian; Ruiz, Eduardo; Salgado-Luarte, Cristian; Molina-Montenegro, Marco A; Gianoli, Ernesto

    2013-01-01

    The climbing habit is a key innovation in angiosperm evolution: climbing plant taxa have greater species richness than their non-climbing sister groups. It is considered that highly diversified clades should show increased among-population genetic differentiation. Less clear is the expected pattern regarding within-population genetic diversity in speciose lineages. We tested the hypothesis of greater within-population genetic diversity in climbing plants compared to trees in a temperate fores...

  5. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

    Directory of Open Access Journals (Sweden)

    Karima Fadhlaoui-Zid

    Full Text Available The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

  6. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

    Science.gov (United States)

    Fadhlaoui-Zid, Karima; Haber, Marc; Martínez-Cruz, Begoña; Zalloua, Pierre; Benammar Elgaaied, Amel; Comas, David

    2013-01-01

    The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

  7. Sleep duration is significantly associated with carotid artery atherosclerosis incidence in a Japanese population.

    Science.gov (United States)

    Abe, Tsueko; Aoki, Toshinari; Yata, Syogo; Okada, Masahiko

    2011-08-01

    Previous studies have indicated that sleep duration is associated with total mortality in a U-shaped fashion. The purpose of the current study was to examine the relationship between self-reported sleep duration and carotid artery atherosclerosis in a Japanese population. In 2009-2010, a total of 2498 participants (1195 men, 1303 women; age range, 23-92 years) were recruited from members of a Japanese community receiving annual health check-up at a local health center who agreed to participate in the study. Exclusion criteria were as follows: age <40 or ≥85 years; and more than one missing value from either laboratory data or questionnaire responses. A total of 2214 participants were entered into the study. Carotid artery arteriosclerosis was evaluated ultrasonographically and quantified as intima-medial thickness (IMT). The presence of carotid artery atherosclerosis was defined as IMT≥1.2 mm. Sleep durations were compared with IMT measurements after controlling for confounding factors such as age, sex, lipid profile, fasting plasma glucose, hemoglobin A1c, blood pressure, alcohol intake, and smoking habit. Sleep duration ≥7 h correlated significantly with the incidence of IMT≥1.2 m when compared with a sleep duration of 6 h (multivariate-adjusted odds ratio, 1.263; 95% confidence interval, 1.031-1.546, P=0.024). Shorter sleep duration ≤5 h did not correlate significantly with the risk compared with a sleep duration of 6 h. Long sleep duration (≥7 h) correlated significantly with the incidence of carotid artery atherosclerosis compared with a sleep duration of 6 h, but shorter sleep duration did not. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  8. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

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    Melissa D Conrad

    Full Text Available Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes.Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2 differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages.Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  9. Extensive genetic diversity, unique population structure and evidence of genetic exchange in the sexually transmitted parasite Trichomonas vaginalis.

    Science.gov (United States)

    Conrad, Melissa D; Gorman, Andrew W; Schillinger, Julia A; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E; Carlton, Jane M

    2012-01-01

    Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease.

  10. Genetic diversity in natural populations of Buriti (Mauritia flexuosa L. f.

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    Liene Rocha Picanço Gomes

    2011-01-01

    Full Text Available This study aimed to characterize the genetic diversity of buriti populations by AFLP (Amplified Fragment LengthPolymorphism markers. The analysis was performed in four populations used by traditional communities in the state of Amazonia(Bom Jesus do Anamã, Lauro Sodré, Santa Luzia do Buiçuzinho, and Esperança II. From each population 30 plants wererandomly selected. To obtain the markers four primer combinations were used. The percentage of polymorphic loci was estimated,the molecular variance among and within populations analyzed and a dendrogram constructed. The primers detected 339 polymorphicloci ranging from 81.1 % to 91.1 % among populations. Analysis of molecular variance attributed 77.18 % to variation within and22.8 % to variation between populations. The dendrogram indicated the formation of two groups, showing that the populations ofBom Jesus do Anamã and Lauro Sodré are genetically most similar and thet the genetic and geographical distances are notcorrelated.

  11. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

    Science.gov (United States)

    Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

    2014-03-20

    Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

  12. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  13. Genetic Diversity and Structure of Natural Quercus variabilis Population in China as Revealed by Microsatellites Markers

    Directory of Open Access Journals (Sweden)

    Xiaomeng Shi

    2017-12-01

    Full Text Available Quercus variabilis is a tree species of ecological and economic value that is widely distributed in China. To effectively evaluate, use, and conserve resources, we applied 25 pairs of simple sequence repeat (SSR primers to study its genetic diversity and genetic structure in 19 natural forest or natural secondary forest populations of Q. variabilis (a total of 879 samples. A total of 277 alleles were detected. Overall, the average expected heterozygosity (He was 0.707 and average allelic richness (AR was 7.79. Q. variabilis manifested a loss of heterozygosity, and the mean of inbreeding coefficient (FIS was 0.044. Less differentiation among populations was observed, and the genetic differentiation coefficient (FST was 0.063. Bayesian clustering analysis indicated that the 19 studied populations could be divided into three groups based on their genetic makeup, namely, the Southwest group, Central group, and Northeastern group. The Central group, compared to the populations of the Southwest and Northeast group, showed higher genetic diversities and lower genetic differentiations. As a widely distributed species, the historical migration of Q. variabilis contributed to its genetic differentiation.

  14. Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L

    Science.gov (United States)

    The crop species Brassica rapa L. has significant economic importance around the globe. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption and fodder for livestock. However, the global distribution and ...

  15. A genomic insight into diversity among tribal and nontribal population groups of Manipur, India.

    Science.gov (United States)

    Saraswathy, K N; Kiranmala, Naorem; Murry, Benrithung; Sinha, Ekata; Saksena, Deepti; Kaur, Harpreet; Sachdeva, M P; Kalla, A K

    2009-10-01

    Twenty autosomal markers, including linked markers at two gene markers, are used to understand the genomic similarity and diversity among three tribal (Paite, Thadou, and Kom) and one nontribal communities of Manipur (Northeast India). Two of the markers (CD4 and HB9) are monomorphic in Paite and one (the CD4 marker) in Kom. Data suggest the Meitei (nontribal groups) stand apart from the three tribal groups with respect to higher heterozygosity (0.366) and presence of the highest ancestor haplotypes of DRD2 markers (0.228); this is also supported by principal co-ordinate analysis. These populations are found to be genomically closer to the Chinese population than to other Indian populations.

  16. Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

    Science.gov (United States)

    Regidor-Cerrillo, Javier; Díez-Fuertes, Francisco; García-Culebras, Alicia; Moore, Dadín P.; González-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Díaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

    2013-01-01

    The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal

  17. Diversity and convergence of population aging: evidence from China and Canada

    Directory of Open Access Journals (Sweden)

    Légaré, Jacques

    2004-01-01

    Full Text Available EnglishTaking the diversity and the convergence of demographic transitions intoconsideration, it is hypothesized that population aging that occurs in developed countries anddeveloping countries will reflect diversity, but will also show some convergence. In order to testthis hypothesis, the present study compares the population aging experiences of China (1971-2050 andCanada (1911-2050 and places them within the context of the demographic transition. In this paper welearn how, as population ages, these two countries will, through two distinct pathways, arrive atsimilar age structures by the middle of the 21st century. Both the diversity and the convergence ofpopulation aging are shown in this comparative study.FrenchEn constatant la diversité et la convergence des transitions démographiques,nous faisons l'hypothèse que le processus du vieillissement démographiquecomporte également une certaine diversité et montrera une convergence, enparticulier, entre les pays développés et les pays en développement. Afin devérifier cette hypothèse, la présente étude compare les vieillissementsdémographiques en Chine (1971-2050 et au Canada (1911-2050, en lesmettant dans le contexte de la transition démographique. Cet article montre qu’àmesure que vieillit la population, comment ces deux pays arriveront par deuxvoies distinctes à une structure par âge similaire au milieu du XXIème siècle. Ladiversité et la convergence du vieillissement sont toutes deux illustrées danscette étude comparative.

  18. The role of viral population diversity in adaptation of bovine coronavirus to new host environments.

    Directory of Open Access Journals (Sweden)

    Monica K Borucki

    Full Text Available The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing and 38,000×(Illumina. The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were "selected" from a pre-existing pool rather than through de novo mutation and subsequent population fixation.

  19. Highly diverse recombining populations of Vibrio cholerae and Vibrio parahaemolyticus in French Mediterranean coastal lagoons

    Directory of Open Access Journals (Sweden)

    Kevin eEsteves

    2015-07-01

    Full Text Available Vibrio parahaemolyticus and Vibrio cholerae are ubiquitous to estuarine and marine environments. These two species can induce infections in humans. Therefore understanding the structure and dynamics of non-pandemic environmental populations in temperate regions, such as Mediterranean coastal systems, is important if we are to evaluate the risks of infection to humans.Environmental isolates of V. cholerae (n=109 and V. parahaemolyticus (n=89 sampled at different dates, stations and water salinities were investigated for virulence genes and by a multilocus sequence-based analysis (MLSA. V. cholerae isolates were all ctxA negative and only one isolate of V. parahaemolyticus displayed trh2 gene. Most Sequence Types (ST corresponded to unique ST isolated at one date or one station. Frequent recombination events were detected among different pathogenic species, V. parahaemolyticus, V. cholerae, Vibrio mimicus and Vibrio metoecus. Recombination had a major impact on the diversification of lineages. The genetic diversity assessed by the number of ST/strain was higher in low salinity conditions for V. parahaemolyticus and V. cholerae whereas the frequency of recombination events in V. cholerae was lower in low salinity. Mediterranean coastal lagoon systems housed V. cholerae and V. parahaemolyticus with genetic diversities equivalent to the worldwide diversity described so far. The presence of STs found in human infections as well as the frequency of recombination events in environmental vibrios populations could predict a potential epidemiological risk.

  20. Genetic diversity and population structure of Lantana camara in India indicates multiple introductions and gene flow.

    Science.gov (United States)

    Ray, A; Quader, S

    2014-05-01

    Lantana camara is a highly invasive plant, which has spread over 60 countries and island groups of Asia, Africa and Australia. In India, it was introduced in the early nineteenth century, since when it has expanded and gradually established itself in almost every available ecosystem. We investigated the genetic diversity and population structure of this plant in India in order to understand its introduction, subsequent range expansion and gene flow. A total of 179 individuals were sequenced at three chloroplast loci and 218 individuals were genotyped for six nuclear microsatellites. Both chloroplasts (nine haplotypes) and microsatellites (83 alleles) showed high genetic diversity. Besides, each type of marker confirmed the presence of private polymorphism. We uncovered low to medium population structure in both markers, and found a faint signal of isolation by distance with microsatellites. Bayesian clustering analyses revealed multiple divergent genetic clusters. Taken together, these findings (i.e. high genetic diversity with private alleles and multiple genetic clusters) suggest that Lantana was introduced multiple times and gradually underwent spatial expansion with recurrent gene flow. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties.

    Science.gov (United States)

    Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

    2014-01-01

    Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.

  2. Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L. varieties.

    Directory of Open Access Journals (Sweden)

    Nanna Hellum Nielsen

    Full Text Available Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT was used to characterize a population of 94 bread wheat (Triticum aestivum L. varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA. These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8 locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents.

  3. Evaluation of genetic diversity in wild populations of Peganum harmala L., a medicinal plant

    Directory of Open Access Journals (Sweden)

    Ranya EL-Bakatoushi

    2018-06-01

    Full Text Available Peganum harmala L. is a perennial herbaceous plant and can be a future drug due to its wide medicinal purposes. Despite its economic importance, the molecular genetics of P. harmal have not yet been studied in detail. Genetic diversity of 12 P. harmala genotypes were investigated by using Inter-Simple Sequence Repeats (ISSR, PCR-RFLP of rDNA-ITS, PCR-SSCP of rDNA-ITS and Simple Sequence Repeat (SSR markers. The level of polymorphism revealed by ITS-SSCP is the lowest, followed by ITS-RFLP then ISSR and the highest polymorphism level was reported for SSR marker. The AMOVA analysis implied that most of the variation occurred within the Populations. A value of inbreeding coefficient Fis estimated by the three co-dominant markers was nearly equal and offer an indication of the partial out-crossing reproductive system of P. harmala. Principal Coordinate Analysis (PCOA plot revealed a clear pattern of clustering based on the locations of collected plants which coincide with the isolation by distance. The study revealed that ITS-SSCP and ISSR markers respectively were more informative than the other used markers in the assessment of genetic diversity of P. harmala. The results reflect the great diversity of P. harmala and data obtained from this study can be used for future collecting missions. Keywords: Peganum harmala, Genetic diversity, ISSR, rDNA-ITS, SSR

  4. Population genetic structure of Taenia solium from Madagascar and Mexico: implications for clinical profile diversity and immunological technology.

    Science.gov (United States)

    Vega, Rodrigo; Piñero, Daniel; Ramanankandrasana, Bienvenue; Dumas, Michel; Bouteille, Bernard; Fleury, Agnes; Sciutto, Edda; Larralde, Carlos; Fragoso, Gladis

    2003-11-01

    Taenia solium is a cestode parasitic of humans and pigs that strongly impacts on public health in developing countries. Its larvae (cysticercus) lodge in the brain, causing neurocysticercosis, and in other tissues, like skeletal muscle and subcutaneous space, causing extraneuronal cysticercosis. Prevalences of these two clinical manifestations vary greatly among continents. Also, neurocysticercosis may be clinically heterogeneous, ranging from asymptomatic forms to severely incapacitating and even fatal presentation. Further, vaccine design and diagnosis technology have met with difficulties in sensitivity, specificity and reproducibility. Parasite diversity underlying clinical heterogeneity and technological difficulties is little explored. Here, T. solium genetic population structure and diversity was studied by way of random amplified polymorphic DNA in individual cysticerci collected from pigs in Madagascar and two regions in Mexico. The amplification profiles of T. solium were also compared with those of the murine cysticercus Taenia crassiceps (ORF strain). We show significant genetic differentiation between Madagascar and Mexico and between regions in Mexico, but less so between cysticerci from different localities in Mexico and none between cysticerci from different tissues from the same pig. We also found restricted genetic variability within populations and gene flow was estimated to be low between populations. Thus, genetic differentiation of T. solium suggests that different evolutionary paths have been taken and provides support for its involvement in the differential tissue distribution of cysticerci and varying degrees of severity of the disease. It may also explain difficulties in the development of vaccines and tools for immunodiagnosis.

  5. The effect of multiple paternity on genetic diversity of small populations during and after colonisation.

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    Marina Rafajlović

    Full Text Available Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration has been reached. During colonisation, multiple mating by [Formula: see text] males increased the heterozygosity by [Formula: see text] in comparison with single paternity, while in the steady state the increase was [Formula: see text] compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity.

  6. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Directory of Open Access Journals (Sweden)

    Damian Labuda

    Full Text Available The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  7. X-linked MTMR8 diversity and evolutionary history of sub-Saharan populations.

    Science.gov (United States)

    Labuda, Damian; Yotova, Vania; Lefebvre, Jean-François; Moreau, Claudia; Utermann, Gerd; Williams, Scott M

    2013-01-01

    The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ~500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

  8. The Effect of Multiple Paternity on Genetic Diversity of Small Populations during and after Colonisation

    KAUST Repository

    Rafajlović, Marina

    2013-10-28

    Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration) has been reached. During colonisation, multiple mating by 2-10 males increased the heterozygosity by 10-300% in comparison with single paternity, while in the steady state the increase was 10-50% compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity. 2013 Rafajlovi? et al.

  9. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

    Directory of Open Access Journals (Sweden)

    J. F. Vázquez-Armijo

    2017-06-01

    Full Text Available The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

  10. The prevalence and prognostic significance of KRAS mutation subtypes in lung adenocarcinomas from Chinese populations

    Directory of Open Access Journals (Sweden)

    Zheng DF

    2016-02-01

    Full Text Available Difan Zheng,1,2,* Rui Wang,1,2,* Yang Zhang,1,2 Yunjian Pan,1,2 Xinghua Cheng,3 Chao Cheng,1,2 Shanbo Zheng,1,2 Hang Li,1,2 Ranxia Gong,1,2 Yuan Li,2,4 Xuxia Shen,2,4 Yihua Sun,1,2 Haiquan Chen1–3,51Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 2Department of Oncology, Shanghai Medical College, Fudan University, 3Shanghai Chest Hospital, Shanghai Jiao Tong University, 4Department of Pathology, Fudan University Shanghai Cancer Center, 5Institutes of Biomedical Sciences, Fudan University, Shanghai, People’s Republic of China*These authors contributed equally to this workBackground: We performed this retrospective study to identify the prevalence of KRAS mutation in Chinese populations and make a comprehensive investigation of the clinicopathological features of KRAS mutation in these patients.Patients and methods: Patients from 2007 to 2013 diagnosed with primary lung adenocarcinoma who received a radical resection were examined for KRAS, EGFR, HER2, BRAF mutations, and ALK, RET, and ROS1 fusions. Clinicopathological features, including sex, age, tumor–lymph node–metastasis stage, tumor differentiation, smoking status, histological subtypes, and survival information were analyzed.Result: KRAS mutation was detected in 113 of 1,368 patients. Nine different subtypes of KRAS mutation were identified in codon 12, codon 13, and codon 61. KRAS mutation was more frequently found in male patients and former/current smoker patients. Tumors with KRAS mutation had poorer differentiation. Invasive mucinous adenocarcinoma predominant and solid predominant subtypes were more frequent in KRAS mutant patients. No statistical significance was found in relapse-free survival or overall survival between patients with KRAS mutation and patients with other mutations.Conclusion: In Chinese populations, we identified KRAS mutation in 8.3% (113/1,368 of the patients with lung adenocarcinoma. KRAS mutation defines a molecular subset of

  11. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

    Directory of Open Access Journals (Sweden)

    Raymond Kiu

    2017-12-01

    Full Text Available Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc, enterotoxin (cpe, and Perfringolysin O (pfo or pfoA, although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56 of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet and anti-defensins genes (mprF were consistently detected in silico (tet: 75%; mprF: 100%. However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  12. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.

    Science.gov (United States)

    Kiu, Raymond; Caim, Shabhonam; Alexander, Sarah; Pachori, Purnima; Hall, Lindsay J

    2017-01-01

    Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens -associated exotoxins genes including α-toxin ( plc ), enterotoxin ( cpe ), and Perfringolysin O ( pfo or pfoA ), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes ( tet ) and anti-defensins genes ( mprF ) were consistently detected in silico ( tet : 75%; mprF : 100%). However, pre-antibiotic era strain genomes did not encode for tet , thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  13. Genetic diversity in the desert warthog (Phacochoerus aethiopicus delameri) population of eastern Africa

    DEFF Research Database (Denmark)

    Muwanika, Vincent B.; Kock, Richard; Masembe, Charles

    2012-01-01

    in a population of the desert warthog (Phacochoerus aethiopicus) sampled from 12 localities in its natural range in eastern Africa. From the total sample (30 individuals), at the six microsatellite loci that were analysed, a total of 43 alleles was observed averaging seven alleles per locus. Expected...... heterozygosity (HE) per locus was high, ranging from 0.53 to 0.87. At the mitochondrial loci, nucleotide diversity was low (p = 0.12%) with two unique haplotypes observed from the 19 individuals that amplified successfully. The diversity indices observed in the desert warthog are comparable to those previously...... reported for the closely related but widespread species, the common warthog (Phacochoerus africanus). These results suggest that the desert warthog is not genetically depauperate despite the rinderpest epidemic of the 1880s that eliminated it from most of its natural range....

  14. Ecological significance of microsatellite variation in western North American populations of Bromus tectorum

    Science.gov (United States)

    Alisa P. Ramakrishnan; Susan Meyer; Daniel J. Fairbanks; Craig E. Coleman

    2006-01-01

    Bromus tectorum (cheatgrass or downy brome) is an exotic annual weed that is abundant in western USA. We examined variation in six microsatellite loci for 17 populations representing a range of habitats in Utah, Idaho, Nevada and Colorado (USA) and then intensively sampled four representative populations, for a total sample size of approximately 1000 individuals. All...

  15. Some Chronic Rhinosinusitis Patients Have Significantly Elevated Populations of Seven Fungi in their Sinuses

    Science.gov (United States)

    Abstract: Objectives/Hypothesis: To measure the populations of 36 fungi in the homes and sinuses of chronic rhinosinusitis (CRS) and non-CRS patients. Study Design: Single-blind cross-sectional study. Methods: Populations of 36 fungi were measured in sinus samples and in the home...

  16. Allozyme and RAPD Analysis of the Genetic Diversity and Geographic Variation in Wild Populations of the American Chestnut (Fagaceae)

    Science.gov (United States)

    Hongwen Huang; Fenny Dane; Thomas L. Kubisiak

    1998-01-01

    Genetic variation among 12 populations of the American chestnut (Custanea dentata) was investigated. Population genetic parameters estimated from allozyme variation suggest that C. dentata at both the population and species level has narrow genetic diversity as compared to other species in the genus. Average expected heterozygosity...

  17. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China.

    Science.gov (United States)

    Zheng, D-J; Xie, L-S; Zhu, J-H; Zhang, Z-L

    2012-09-01

    Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  18. The prevalence of malnutrition according to the new ESPEN definition in four diverse populations.

    Science.gov (United States)

    Rojer, A G M; Kruizenga, H M; Trappenburg, M C; Reijnierse, E M; Sipilä, S; Narici, M V; Hogrel, J Y; Butler-Browne, G; McPhee, J S; Pääsuke, M; Meskers, C G M; Maier, A B; de van der Schueren, M A E

    2016-06-01

    Consensus on the definition of malnutrition has not yet been reached. Recently, The European Society for Clinical Nutrition and Metabolism (ESPEN) proposed a consensus definition of malnutrition. The aim of the present study was to describe the prevalence of malnutrition according to the ESPEN definition in four diverse populations. In total, 349 acutely ill middle-aged patients, 135 geriatric outpatients, 306 healthy old individuals and 179 healthy young individuals were included in the study. Subjects were screened for risk of malnutrition using the SNAQ. The ESPEN definition of malnutrition, i.e. low BMI (malnutrition. The prevalence of malnutrition ranged from 0% in the healthy young, 0.5% in healthy old individuals, 6% in the geriatric outpatients to 14% in the acutely ill middle-aged patients. Prevalence of low FFMI was observed in all four populations (14-33%), but concurred less frequently with weight loss (0-13%). Using the ESPEN definition, 0%-14% malnutrition was found in the diverse populations. Further work is needed to fully address the validity of a two-step approach, including risk assessment as an initial step in screening and defining malnutrition. Furthermore, assessing the predictive validity of the ESPEN definition is needed. Copyright © 2015 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  19. Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone.

    Science.gov (United States)

    Beet, Clare R; Hogg, Ian D; Collins, Gemma E; Cowan, Don A; Wall, Diana H; Adams, Byron J

    2016-09-01

    Climate changes are likely to have major influences on the distribution and abundance of Antarctic terrestrial biota. To assess arthropod distribution and diversity within the Ross Sea region, we examined mitochondrial DNA (COI) sequences for three currently recognized species of springtail (Collembola) collected from sites in the vicinity, and to the north of, the Mackay Glacier (77°S). This area acts as a transition between two biogeographic regions (northern and southern Victoria Land). We found populations of highly divergent individuals (5%-11.3% intraspecific sequence divergence) for each of the three putative springtail species, suggesting the possibility of cryptic diversity. Based on molecular clock estimates, these divergent lineages are likely to have been isolated for 3-5 million years. It was during this time that the Western Antarctic Ice Sheet (WAIS) was likely to have completely collapsed, potentially facilitating springtail dispersal via rafting on running waters and open seaways. The reformation of the WAIS would have isolated newly established populations, with subsequent dispersal restricted by glaciers and ice-covered areas. Given the currently limited distributions for these genetically divergent populations, any future changes in species' distributions can be easily tracked through the DNA barcoding of springtails from within the Mackay Glacier ecotone.

  20. Genetic diversity and population structure in the Leishmania guyanensis vector Lutzomyia anduzei (Diptera, Psychodidae) from the Brazilian Amazon.

    Science.gov (United States)

    Scarpassa, Vera Margarete; Figueiredo, Adrya da Silva; Alencar, Ronildo Baiatone

    2015-04-01

    Lutzomyia (Nyssomyia) anduzei has been recognized as a secondary vector of Leishmania guyanensis in the Brazilian Amazon region. Since L. anduzei is anthropophilic, co-exists in areas of high leishmaniasis transmission and has been found infected with L. guyanensis, the understanding of the vector population structure and of the process responsible for it is paramount to the vector management and control efforts. In this study we analyzed 74 and 67 sequences of the COI and Cytb loci, respectively, from mitochondrial DNA, aiming to estimate the intra-population genetic variability and population structure in six L. anduzei samples from the Brazilian Amazon region. For COI, we found 58 haplotypes, low to high (FST=0.0310-0.4128) and significant (P=0.0033) genetic structure, and reduced gene flow among populations. The haplotype network yielded many reticulations that likely resulted from hypervariability in the locus. For Cytb, we observed 27 haplotypes, low to moderate (FST=0.0077-0.1954) and nonsignificant (P>0.05) genetic structure for the majority of comparisons and extensive gene flow among populations, in line with the haplotypes network data. AMOVA analysis indicated that most of the variation occurred within populations (83.41%, 90.94%); nevertheless, there were significant differences (ΦST=0.0906-0.1659; P=0.00098; P=0.00000) among them for both loci. The Mantel test showed that the genetic structure is not associated to an isolation-by-distance (IBD) model in either of both loci. These data suggest that L. anduzei is genetically very diverse. The genetic structure lacking IBD may be due to adaptation to local habitats and the low dispersal capacity of the sandflies, and both could lead to population fragmentation and geographic isolation. These findings have important implications for epidemiology, surveillance and vector control and may be a first step in understanding the evolutionary history of this species. Copyright © 2015 Elsevier B.V. All rights

  1. TCF7L2 variant genotypes and type 2 diabetes risk in Brazil: significant association, but not a significant tool for risk stratification in the general population

    Directory of Open Access Journals (Sweden)

    Mill JG

    2008-12-01

    Full Text Available Abstract Background Genetic polymorphisms of the TCF7L2 gene are strongly associated with large increments in type 2 diabetes risk in different populations worldwide. In this study, we aimed to confirm the effect of the TCF7L2 polymorphism rs7903146 on diabetes risk in a Brazilian population and to assess the use of this genetic marker in improving diabetes risk prediction in the general population. Methods We genotyped the single nucleotide polymorphisms (SNP rs7903146 of the TCF7L2 gene in 560 patients with known coronary disease enrolled in the MASS II (Medicine, Angioplasty, or Surgery Study Trial and in 1,449 residents of Vitoria, in Southeast Brazil. The associations of this gene variant to diabetes risk and metabolic characteristics in these two different populations were analyzed. To access the potential benefit of using this marker for diabetes risk prediction in the general population we analyzed the impact of this genetic variant on a validated diabetes risk prediction tool based on clinical characteristics developed for the Brazilian general population. Results SNP rs7903146 of the TCF7L2 gene was significantly associated with type 2 diabetes in the MASS-II population (OR = 1.57 per T allele, p = 0.0032, confirming, in the Brazilian population, previous reports of the literature. Addition of this polymorphism to an established clinical risk prediction score did not increased model accuracy (both area under ROC curve equal to 0.776. Conclusion TCF7L2 rs7903146 T allele is associated with a 1.57 increased risk for type 2 diabetes in a Brazilian cohort of patients with known coronary heart disease. However, the inclusion of this polymorphism in a risk prediction tool developed for the general population resulted in no improvement of performance. This is the first study, to our knowledge, that has confirmed this recent association in a South American population and adds to the great consistency of this finding in studies around the world

  2. Genetic diversity and genetic structure of farmed and wild Chinese mitten crab (Eriocheir sinensis) populations from three major basins by mitochondrial DNA COI and Cyt b gene sequences.

    Science.gov (United States)

    Zhang, Cheng; Li, Qingqing; Wu, Xugan; Liu, Qing; Cheng, Yongxu

    2017-11-20

    The Chinese mitten crab, Eriocheir sinensis, is one of the important native crab species in East Asian region, which has been widely cultured throughout China, particularly in river basins of Yangtze, Huanghe and Liaohe. This study was designed to evaluate the genetic diversity and genetic structure of cultured and wild E. sinensis populations from the three river basins based on mitochondrial DNA (mtDNA) cytochrome oxidase subunit I (COI) and cytochrome b (Cyt b). The results showed that there were 62 variable sites and 30 parsimony informative sites in the 647 bp of sequenced mtDNA COI from 335 samples. Similarly, a 637 bp segment of Cyt b provided 59 variable sites and 26 parsimony informative sites. AMOVA showed that the levels of genetic differentiation were low among six populations. Although the haplotype diversity and nucleotide diversity of Huanghe wild population had slightly higher than the other populations, there were no significant differences. There was no significant differentiation between the genetic and geographic distance of the six populations, and haplotype network diagram indicated that there may exist genetic hybrids of E. sinensis from different river basins. The results of clustering and neutrality tests revealed that the distance of geographical locations were not completely related to their genetic distance values for the six populations. In conclusion, these results have great significance for the evaluation and exploitation of germplasm resources of E. sinensis.

  3. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

    Directory of Open Access Journals (Sweden)

    Sonia E. Eynard

    2018-01-01

    Full Text Available Genomic selection (GS is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

  4. Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs.

    Science.gov (United States)

    Eynard, Sonia E; Croiseau, Pascal; Laloë, Denis; Fritz, Sebastien; Calus, Mario P L; Restoux, Gwendal

    2018-01-04

    Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations. Copyright © 2018 Eynard et al.

  5. Genetic Diversity and Distribution of Blastocystis Subtype 3 in Human Populations, with Special Reference to a Rural Population in Central Mexico

    Directory of Open Access Journals (Sweden)

    Liliana Rojas-Velázquez

    2018-01-01

    Full Text Available Blastocystis subtype 3 (ST3 is a parasitic protist found in the digestive tract of symptomatic and asymptomatic humans around the world. While this parasite exhibits a high prevalence in the human population, its true geographic distribution and global genetic diversity are still unknown. This gap in knowledge limits the understanding of the spread mechanisms, epidemiology, and impact that this parasite has on human populations. Herein, we provided new data on the geographical distribution and genetic diversity of Blastocystis ST3 from a rural human population in Mexico. To do so, we collected and targeted the SSU-rDNA region in fecal samples from this population and further compared its genetic diversity and structure with that previously observed in populations of Blastocystis ST3 from other regions of the planet. Our analyses reveled that diversity of Blastocystis ST3 showed a high haplotype diversity and genetic structure to the world level; however, they were low in the Morelos population. The haplotype network revealed a common widespread haplotype from which the others were generated recently. Finally, our results suggested a recent expansion of the diversity of Blastocystis ST3 worldwide.

  6. Population structure and diversity of citrus tristeza virus (CTV) isolates in Hunan province, China.

    Science.gov (United States)

    Xiao, Cui; Yao, Run-Xian; Li, Fang; Dai, Su-Ming; Licciardello, Grazia; Catara, Antonino; Gentile, Alessandra; Deng, Zi-Niu

    2017-02-01

    Stem-pitting (SP) is the main type of citrus tristeza virus (CTV) that causes severe damage to citrus trees, especially those of sweet orange, in Hunan province, China. Understanding the local CTV population structure should provide clues for effective mild strain cross-protection (MSCP) of the SP strain of CTV. In this study, markers for the p23 gene, multiple molecular markers (MMMs), and sequence analysis of the three silencing suppressor genes (p20, p23 and p25) were employed to analyze the genetic diversity and genotype composition of the CTV population based on 51 CTV-positive samples collected from 14 citrus orchards scattered around six major citrus-growing areas of Hunan. The results indicated that the CTV population structure was extremely complex and that infection was highly mixed. In total, p23 gene markers resulted in six profiles, and MMMs demonstrated 25 profiles. The severe VT and T3 types appeared to be predominantly associated with SP, while the mild T30 and RB types were related to asymptomatic samples. Based on phylogenetic analysis of the amino acid sequences of p20, p23 and p25, 19 representative CTV samples were classified into seven recently established CTV groups and a potentially novel one. A high level of genetic diversity, as well as potential recombination, was revealed among different CTV isolates. Five pure SP severe and two pure mild strains were identified by genotype composition analysis. Taken together, the results update the genetic diversity of CTV in Hunan with the detection of one possible novel strain, and this information might be applicable for the selection of appropriate mild CTV strains for controlling citrus SP disease through cross-protection.

  7. Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae across Its Native Range.

    Directory of Open Access Journals (Sweden)

    Karl T Lund

    Full Text Available Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA. These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might

  8. Population Structure, Diversity and Reproductive Mode of the Grape Phylloxera (Daktulosphaira vitifoliae) across Its Native Range.

    Science.gov (United States)

    Lund, Karl T; Riaz, Summaira; Walker, M Andrew

    2017-01-01

    Grape Phylloxera, Daktulosphaira vitifoliae, is a gall-forming insect that feeds on the leaves and roots of many Vitis species. The roots of the cultivated V. vinifera cultivars and hybrids are highly susceptible to grape phylloxera feeding damage. The native range of this insect covers most of North America, and it is particularly abundant in the eastern and central United States. Phylloxera was introduced from North America to almost all grape-growing regions across five of the temperate zone continents. It devastated vineyards in each of these regions causing large-scale disruptions to grape growers, wine makers and national economies. In order to understand the population diversity of grape phylloxera in its native range, more than 500 samples from 19 States and 34 samples from the introduced range (northern California, Europe and South America) were genotyped with 32 simple sequence repeat markers. STRUCTURE, a model based clustering method identified five populations within these samples. The five populations were confirmed by a neighbor-joining tree and principal coordinate analysis (PCoA). These populations were distinguished by their Vitis species hosts and their geographic locations. Samples collected from California, Europe and South America traced back to phylloxera sampled in the northeastern United States on V. riparia, with some influence from phylloxera collected along the Atlantic Coast and Central Plains on V. vulpina. Reproductive statistics conclusively confirmed that sexual reproduction is common in the native range and is combined with cyclical parthenogenesis. Native grape phylloxera populations were identified to be under Hardy-Weinberg equilibrium. The identification of admixed samples between many of these populations indicates that shared environments facilitate sexual reproduction between different host associated populations to create new genotypes of phylloxera. This study also found that assortative mating might occur across the

  9. Results of efforts by the Convention on Biological Diversity to describe ecologically or biologically significant marine areas.

    Science.gov (United States)

    Bax, Nicholas J; Cleary, Jesse; Donnelly, Ben; Dunn, Daniel C; Dunstan, Piers K; Fuller, Mike; Halpin, Patrick N

    2016-06-01

    In 2004, Parties to the Convention on Biological Diversity (CBD) addressed a United Nations (UN) call for area-based planning, including for marine-protected areas that resulted in a global effort to describe ecologically or biologically significant marine areas (EBSAs). We summarized the results, assessed their consistency, and evaluated the process developed by the Secretariat of the CBD to engage countries and experts in 9 regional workshops held from 2011 to 2014. Experts from 92 countries and 79 regional or international bodies participated. They considered 250 million km(2) of the world's ocean area (two-thirds of the total). The 204 areas they examined in detail differed widely in area (from 5.5 km(2) to 11.1 million km(2) ). Despite the initial focus of the CBD process on areas outside national jurisdiction, only 31 of the areas examined were solely outside national jurisdiction. Thirty-five extended into national jurisdictions, 137 were solely within national jurisdictions, and 28 included the jurisdictions of more than 1 country (1 area lacked precise boundaries). Data were sufficient to rank 88-99% of the areas relative to each of the 7 criteria for EBSAs agreed to previously by Parties to the CBD. The naturalness criterion ranked high for a smaller percentage of the EBSAs (31%) than other criteria (51-70%), indicating the difficulty in finding relatively undisturbed areas in the ocean. The highly participatory nature of the workshops, including easy and consistent access to the relevant information facilitated by 2 technical teams, contributed to the workshop participants success in identifying areas that could be ranked relative to most criteria and areas that extend across jurisdictional boundaries. The formal recognition of workshop results by the Conference of Parties to the CBD resulted in these 204 areas being identified as EBSAs by the 196 Parties. They represent the only suite of marine areas recognized by the international community for their

  10. Genetic diversity of Casearia sylvestris populations in remnants of the Atlantic Forest.

    Science.gov (United States)

    Araujo, F L; Siqueira, M V B M; Grando, C; Viana, J P G; Pinheiro, J B; Alves-Pereira, A; Campos, J B; Brancalion, P H S; Zucchi, M I

    2017-01-23

    Guaçatonga (Casearia sylvestris) is a native plant of the Atlantic Forest, with high medicinal potential and relevance for reforestation programs. The aim of this study was to characterize, with microsatellite markers, two populations of C. sylvestris from remaining areas of the Atlantic Forest in the State of São Paulo. High allelic variation was found in both populations (N A = 101 and 117; A R = 12.5 and 14.4), although with high endogamy coefficients (f = 0.640 and 0.363). Estimates of genetic structure suggested the presence of considerable genetic divergence between the populations (F ST = 0.103); however, there was no spatial genetic structure within the populations. Genetic divergence may have occurred due to decreased gene flow between the fragmented populations as the result of deforestation. The results of this study demonstrate the importance of genetic diversity and its characterization in native plants within remaining forest areas for the management and restoration of such areas.

  11. Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations.

    Science.gov (United States)

    Feusier, Julie; Witherspoon, David J; Scott Watkins, W; Goubert, Clément; Sasani, Thomas A; Jorde, Lynn B

    2017-01-01

    Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements. Combining multiple discovery approaches may provide a better profile of the polymorphic Alu mobilome. Alu Yb8/9 elements have been a focus of our recent studies as they are young subfamilies (~2.3 million years old) that contribute ~30% of recent polymorphic Alu retrotransposition events. Here, we update our ME-Scan methods for detecting Alu elements and apply these methods to discover new insertions in a large set of individuals with diverse ancestral backgrounds. We identified 5,288 putative Alu insertion events, including several hundred novel Alu Yb8/9 elements from 213 individuals from 18 diverse human populations. Hundreds of these loci were specific to continental populations, and 23 non-reference population-specific loci were validated by PCR. We provide high-quality sequence information for 68 rare Alu Yb8/9 elements, of which 11 have hallmarks of an active source element. Our subfamily distribution of rare Alu Yb8/9 elements is consistent with previous datasets, and may be representative of rare loci. We also find that while ME-Scan and low-coverage, whole-genome sequencing (WGS) detect different Alu elements in 41 1000 Genomes individuals, the two methods yield similar population structure results. Current in-silico methods for Alu discovery may miss rare, polymorphic Alu elements. Therefore, using multiple techniques can provide a more accurate profile of Alu elements in individuals and populations. We improved our false-negative rate as an indicator of sample quality for future

  12. Combination of genetics and spatial modelling highlights the sensitivity of cod (Gadus morhua) population diversity in the North Sea to distributions of fishing

    DEFF Research Database (Denmark)

    Heath, Michael R.; Culling, Mark A.; Crozier, Walter W.

    2014-01-01

    Conserving genetic diversity in animal populations is important for sustaining their ability to respond to environmental change. However, the “between-population” component of genetic diversity (biocomplexity) is threatened in many exploited populations, particularly marine fish, where harvest ma...

  13. Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data

    Directory of Open Access Journals (Sweden)

    Zhan Shen

    2017-03-01

    Conclusions: Microsatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.

  14. Genetic diversity of wild and hatchery lake trout populations: Relevance for management and restoration in the Great Lakes

    Science.gov (United States)

    Page, K.S.; Scribner, K.T.; Burnham-Curtis, M.

    2004-01-01

    The biological diversity of lake trout Salvelinus namaycush in the upper Great Lakes was historically high, consisting of many recognizable morphological types and discrete spawning populations. During the 1950s and 1960s, lake trout populations were extirpated from much of the Great Lakes primarily as a result of overfishing and predation by the parasitic sea lamprey Petromyzon marinus. Investigations of how genetic diversity is partitioned among remnant wild lake trout populations and hatchery broodstocks have been advocated to guide lake trout management and conservation planning. Using microsatellite genetic markers, we estimated measures of genetic diversity and the apportionment of genetic variance among 6 hatchery broodstocks and 10 wild populations representing three morphotypes (lean, humper, and siscowet). Analyses revealed that different hatchery broodstocks and wild populations contributed disproportionally to the total levels of genetic diversity. The genetic affinities of hatchery lake trout reflected the lake basins of origin of the wild source populations. The variance in allele frequency over all sampled extant wild populations was apportioned primarily on the basis of morphotype (??MT = 0.029) and secondarily among geographically dispersed populations within each morphotype (??ST = 0.024). The findings suggest that the genetic divergence reflected in recognized morphotypes and the associated ecological and physiological specialization occurred prior to the partitioning of large proglacial lakes into the Great Lakes or as a consequence of higher contemporary levels of gene flow within than among morphotypes. Information on the relative contributions of different broodstocks to total gene diversity within the regional hatchery program can be used to prioritize the broodstocks to be retained and to guide future stocking strategies. The findings highlight the importance of ecological and phenotypic diversity in Great Lakes fish communities and

  15. Cercospora zeina from Maize in South Africa Exhibits High Genetic Diversity and Lack of Regional Population Differentiation.

    Science.gov (United States)

    Muller, Mischa F; Barnes, Irene; Kunene, Ncobile T; Crampton, Bridget G; Bluhm, Burton H; Phillips, Sonia M; Olivier, Nicholas A; Berger, Dave K

    2016-10-01

    South Africa is one of the leading maize-producing countries in sub-Saharan Africa. Since the 1980s, Cercospora zeina, a causal agent of gray leaf spot of maize, has become endemic in South Africa, and is responsible for substantial yield reductions. To assess genetic diversity and population structure of C. zeina in South Africa, 369 isolates were collected from commercial maize farms in three provinces (KwaZulu-Natal, Mpumalanga, and North West). These isolates were evaluated with 14 microsatellite markers and species-specific mating type markers that were designed from draft genome sequences of C. zeina isolates from Africa (CMW 25467) and the United States (USPA-4). Sixty alleles were identified across 14 loci, and gene diversity values within each province ranged from 0.18 to 0.35. High levels of gene flow were observed (Nm = 5.51), and in a few cases, identical multilocus haplotypes were found in different provinces. Overall, 242 unique multilocus haplotypes were identified with a low clonal fraction of 34%. No distinct population clusters were identified using STRUCTURE, principal coordinate analysis, or Weir's theta θ statistic. The lack of population differentiation was supported by analysis of molecular variance tests, which indicated that only 2% of the variation was attributed to variability between populations from each province. Mating type ratios of MAT1-1 and MAT1-2 idiomorphs from 335 isolates were not significantly different from a 1:1 ratio in all provinces, which provided evidence for sexual reproduction. The draft genome of C. zeina CMW 25467 exhibited a complete genomic copy of the MAT1-1 idiomorph as well as exonic fragments of MAT genes from both idiomorphs. The high level of gene diversity, shared haplotypes at different geographical locations within South Africa, and presence of both MAT idiomorphs at all sites indicates widespread dispersal of C. zeina between maize fields in the country as well as evidence for sexual recombination. The