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Sample records for forest genetic diversity

  1. Biodiversity assessment in forests - from genetic diversity to landscape diversity

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    Granke O

    2009-01-01

    Full Text Available Assessing biodiversity in forests requires a reliable and sustainable monitoring concept, which must include all levels of diversity, the genetic, the species and the landscape level. Diversity studies should not be reduced to quantitative analysis, but qualitative interpretations are an important part for the understanding of the results. Also, the linkage of terrestrial data and remote sensing data as well the implementation of abiotic and biotic data collected on existing monitoring systems are useful sources to analyse cause-effect relationships and interactions between the different aspects of diversity.

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

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    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.

  3. Reduction of Genetic Diversity of the Harpy Eagle in Brazilian Tropical Forests.

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    Aureo Banhos

    Full Text Available Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest.

  4. Utilizing forest tree genetic diversity for an adaptation of forest to climate change

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    Schueler, Silvio; Lackner, Magdalena; Chakraborty, Debojyoti

    2017-04-01

    Since climate conditions are considered to be major determinants of tree species' distribution ranges and drivers of local adaptation, anthropogenic climate change (CC) is expected to modify the distribution of tree species, tree species diversity and the forest ecosystems connected to these species. The expected speed of environmental change is significantly larger than the natural migration and adaptation capacity of trees and makes spontaneous adjustment of forest ecosystems improbable. Planting alternative tree species and utilizing the tree species' intrinsic adaptive capacity are considered to be the most promising adaptation strategy. Each year about 900 million seedlings of the major tree species are being planted in Central Europe. At present, the utilization of forest reproductive material is mainly restricted to nationally defined ecoregions (seed/provenance zones), but when seedlings planted today become adult, they might be maladapted, as the climate conditions within ecoregions changed significantly. In the cooperation project SUSTREE, we develop transnational delineation models for forest seed transfer and genetic conservation based on species distribution models and available intra-specific climate-response function. These models are being connected to national registers of forest reproductive material in order support nursery and forest managers by selecting the appropriate seedling material for future plantations. In the long-term, European and national policies as well as regional recommendations for provenances use need to adapted to consider the challenges of climate change.

  5. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

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    Ilga Porth

    2014-04-01

    Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

  6. Genetic Diversity and Spatial Genetic Structure of an Epiphytic Bromeliad in Costa Rican Montane Secondary Forest Patches

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    Cascante-Marín, A.; Oostermeijer, G.; Wolf, J.; Fuchs, E.J.

    2014-01-01

    Information on genetic variation and its distribution in tropical plant populations relies mainly on studies of ground-rooted species, while genetic information of epiphytic plants is still limited. Particularly, the effect of forest successional condition on genetic diversity and structure of

  7. Fengshui forests conserve genetic diversity: a case study of Phoebe bournei (Hemsl.) Yang in southern China.

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    Ge, Y J; Liu, Y J; Shen, A H; Lin, X C

    2015-01-01

    Fengshui forests (sacred groves) are important in traditional Chinese culture and home to many endangered species. These forests may provide protection for some endangered plant species outside the nature reserves, but little is known about their role in genetic conservation. Using inter-simple sequence repeat (ISSR) markers, we compared the genetic diversity of 6 populations of Phoebe bournei (Hemsl.) Yang, a commercially important woody species, which is under second-class national protection and endemic to China. Samples were collected from the nature reserves and Fengshui forests in southern China. Herein, we show that Fengshui forest populations are capable of maintaining some level of genetic diversity. For nature reserve populations, the average NA and NE were 1.58 and 1.39, respectively; and for Fengshui forests, they were 1.39 and 1.12, respectively. For nature reserve populations, Nei's gene diversity (H) and Shannon's index (I) were 0.32 and 0.11, respectively; and for Fengshui forests, they were 0.22 and 0.07, respectively. We discuss the reasons for the genetic differences between populations of the Fengshui forests and nature reserves and propose conservation strategies for the Fengshui forest.

  8. Genetic diversity of Quercus glandulifera var. brevipetiolata populations in three forest communities with different succession stages

    Institute of Scientific and Technical Information of China (English)

    Junmin LI; Zexin JIN; Qiping GU; Wenyan LOU

    2009-01-01

    In order to understand the relationship between population succession and its genetic behavior, random amplified polymorphic DNA (RAPD) technique was used to analyze the genetic diversity of Quercu glandulifera var.brevipetiolata populations in three forest communities with different succession stages (coniferous forest, coniferous and broad-leaved mixed forest, evergreen broad-leaved forest). The results showed that 145 repetitive loci were produced in 60 individuals of Q. glandulifera using 11 primers, among which 120 loci were polymorphic, and the total percentage of polymorphic loci was 82.76% with an average of 64.14%. Estimated by the Shannon information index, the total genetic diversity of the three populations was 0.4747, with an average of 0.3642, while it was 0.3234, with an average of 0.2484, judged from the Nei index. Judged from percentage of polymorphic loci,Shannon inform at ion index and Nei index, the genetic diversity followed a decreasing order: coniferous forest >broad-leaved mixed forest > evergreen broad-leaved for-est. Analysis of molecular variance (AMOVA) showed that 69.73% of the genetic variance existed within populations and 30.27% of the genetic variance existed among popu-lations. The coefficient of gene differentiation (Gst) was 0.2319 and the gene flow (Nm) was 1.6539. The mean of genetic identity among populations of Q. glandulifera was 0.8501 and the mean of genetic distance was 0.1626. The genetic identity between the Q. glandulifera population in the coniferous forest and that in the coniferous and broad-leaved mixed forest was the highest. UPGMA cluster analysis based on Nei's genetic distance showed that the population in the coniferous forest gathered with that in the coniferous and broad-leaved mixed forest firstly, then with that in the evergreen broad-leaved forest. The genetic structure of Q. glandulifera was not only characteristic of the biological characteristics of this species, but was also influenced by the

  9. Genetic diversity of Lithocarpus harlandii populations in three forest communities with different succession stages

    Institute of Scientific and Technical Information of China (English)

    Jianhui LI; Zexin JIN; Wenyan LOU; Junmin LI

    2008-01-01

    By using random amplified polymorphic DNA (RAPD) technique,this paper studied the genetic diversity and genetic differentiation of Lithocarpus harlandii populations in three forest communities (con-iferous forest, coniferous and broad-leaved mixed forest, and evergreen broad-leaved forest) with different succes-sion stages in Tiantai Mountain in Zhejiang Province.The results showed that a total of 173 repetitive loci were produced in 60 individuals of L. Harlandii by 12 random primers, among which, 152 loci were polymorphic, and the total percentage of polymorphic loci was 87.86%. The average percentage of polymorphic loci of the popula-tions was 65.32%, and their total genetic diversity estimated by Shannon information index was 0.4529,with an average of 0.3458,while that judged from Nei's index was 0.3004, with an average of 0.2320. The percentage of polymorphic loci, Shannon information index, and Nei's index of the populations were in the sequence of coniferous forest community coniferous and broad-leaved mixed forest community evergreen broad-leaved forest community. Analysis of molecular variance (AMOVA) showed that 72.85% of genetic variance was found within the populations,and 27.15% of genetic variance resided among the populations. The coefficient of gene differentiation was 0.2277, and the gene flow was 1.6949. The genetic structure of L. Harlandii was influenced not only by the biological characteristics of this species, but also by the micro-environment of different communities. The mean of genetic identity among three populations of L. Harlandii was 0.8662, and the mean of their genetic distance was 0.1442. The genetic similarity between coniferous and broad-leaved mixed forest community and evergreen broad-leaved forest community was the highest, while that between evergreen broad-leaved forest community and coniferous forest community was the lowest.The unweighted pair group method with arithmeticmean (UPGMA) cluster analysis based on Nei's genetic

  10. Is there a positive relationship between naturalness and genetic diversity in forest tree communities?

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    Wehenkel, C.; Corral-Rivas, J. J.; Castellanos-Bocaz, H. A.; Pinedo-Alvarez, A.

    2009-07-01

    Abstract The concepts of genetic diversity and naturalness are well known as measures of conservation values and as descriptors of state or condition. A lack of research evaluating the relationship between genetic diversity and naturalness in biological communities, along with the possible implications in terms of evolutionary aspects and conservation management, make this subject particularly important as regards forest tree communities.We therefore examined the following hypothesis: the genetic diversity of a central-European tree stand averaged over species increases with the naturalness of the stand, as defined by the Potential Natural Vegetation (PNV). The results obtained show that the hypothesis is unsustainable because differences between the averaged genetic diversities of the unnatural and semi-natural stand classes (69 cases) were mostly non-significant. Moreover in three cases, the average genetic diversity of unnatural stand classes was significantly higher than the average genetic diversity of the semi-natural stand classes. A significantly lower average genetic diversity of unnatural stand class was not detected in the statistical analysis. Thus, the naturalness of a tree species community, as inferred from PNV, does not serve as a straightforward indicator of ecological stability when the genetic diversity and the adaptability of tree species are unknown. (Author) 30 refs.

  11. Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot.

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    Carnaval, Ana Carolina; Hickerson, Michael J; Haddad, Célio F B; Rodrigues, Miguel T; Moritz, Craig

    2009-02-06

    Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.

  12. Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: Climate stability predicts unique genetic diversity.

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    Faye, A; Deblauwe, V; Mariac, C; Richard, D; Sonké, B; Vigouroux, Y; Couvreur, T L P

    2016-12-01

    The tropical rain forests of Central Africa contain high levels of species diversity. Paleovegetation or biodiversity patterns suggested successive contraction/expansion phases on this rain forest cover during the last glacial maximum (LGM). Consequently, the hypothesis of the existence of refugia e.g. habitat stability that harbored populations during adverse climatic periods has been proposed. Understory species are tightly associated to forest cover and consequently are ideal markers of forest dynamics. Here, we used two central African rain forest understory species of the palm genus, Podococcus, to assess the role of past climate variation on their distribution and genetic diversity. Species distribution modeling in the present and at the LGM was used to estimate areas of climatic stability. Genetic diversity and phylogeography were estimated by sequencing near complete plastomes for over 120 individuals. Areas of climatic stability were mainly located in mountainous areas like the Monts de Cristal and Monts Doudou in Gabon, but also lowland coastal forests in southeast Cameroon and northeast Gabon. Genetic diversity analyses shows a clear North-South structure of genetic diversity within one species. This divide was estimated to have originated some 500,000years ago. We show that, in Central Africa, high and unique genetic diversity is strongly correlated with inferred areas of climatic stability since the LGM. Our results further highlight the importance of coastal lowland rain forests in Central Africa as harboring not only high species diversity but also important high levels of unique genetic diversity. In the context of strong human pressure on coastal land use and destruction, such unique diversity hotspots need to be considered in future conservation planning.

  13. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

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    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  14. Low genetic diversity and intrapopulation spatial genetic structure of the Atlantic Forest tree, Esenbeckia leiocarpa Engl. (Rutaceae

    Directory of Open Access Journals (Sweden)

    G. Forti

    2014-12-01

    Full Text Available Studies on population genetics are the key to designing effective in situ management plans for tree species, in particular, those subjected to pressure from anthropogenic processes, such as forest fragmentation and logging. To investigate genetic diversity, inbreeding and intrapopulation spatial genetic structure (SGS in a fragmented population of the insect-pollinated tropical tree, Esenbeckia leiocarpa, we developed specific microsatellite markers for this species and mapped and sampled 100 individuals in a forest plot. Two issues were addressed in particular: (i the level of genetic diversity, inbreeding and effective population size, (ii whether intrapopulation spatial genetic structure exists. Among the 14 loci developed, we only used the three that presented polymorphism to estimate the genetic parameters. Genetic diversity was low, whereby the average number of alleles per locus (A was 3.3 and observed (H0 and expected heterozygosities (He were 0.336 and 0.298, respectively. The average fixation index was significantly higher than zero (F = 0.112, suggesting inbreeding. Significant SGS was found up to 7 m and between 31 to 38 m, indicating that trees growing within these distances may be related. Estimates of the effective population size indicated that the 100 sampled trees correspond to 14 individuals that are neither related nor inbred. Our results suggest that the microsatellite markers developed in this study are suitable for studies on geneticdiversity and structure, mating systems, gene flow and SGS in this species.

  15. Knowing and doing: research leading to action in the conservation of forest genetic diversity of Patagonian temperate forests.

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    Gallo, Leonardo A; Marchelli, Paula; Chauchard, Luis; Peñalba, Marcelo Gonzalez

    2009-08-01

    Researchers dealing with conservation subjects usually do not put the results of their work into practice, even when the primary purpose of their research is the preservation of biodiversity. In the South American temperate forests we identified an area with the highest genetic diversity in Argentina of Nothofagus nervosa, one of the most relevant southern beech species. Based on the information of our scientific study and our recommendations, the authorities of Lanin National Park changed the protection status of this area to avoid logging. The new forestry management plans include consideration of "high genetic diversity" in decisions on where logging will be allowed. Results of our initial genetic study induced the analysis of biodiversity at the species and ecosystems levels, which yielded results similar to our genetic studies. A strong connection among researchers and managers from the onset of our study and the awareness of the former about the importance of the implementation of the research work were key to bridging the gap between conservation research and conservation practice.

  16. Genetic diversity of wild service tree (Sorbus torminalis (L. Crantz population from the Forest District Krzyż

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    Leszek Bednorz

    2013-09-01

    Full Text Available The paper presents the results of the study on genetic diversity of wild service tree population from the Forest District Krzyż, in a context of its use in the programme of conservation and restitution of Sorbus torminalis in the territory of the Regional Directorate of the State Forests in Piła in 2010-2013. Twenty S. torminalis trees growing in the Forestry Dębina were sampled (dormant buds and investigated by utilizing isozyme markers; five loci (MDH-B, ME-A, 6PGD-B, ADH-B, PGM-A proved to be polymorphic and only one (PGM-B was monomorphic. The level of diversity and the genetic structure of the investigated population of S. torminalis justified an appropriateness of its including into the programme ex situ as the source of reproduction material.

  17. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research...

  18. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae), the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

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    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  19. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio-mo...

  20. Forest fragmentation in Vietnam : Effects on tree diversity, populations and genetics

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    Ha, V.T.

    2015-01-01

    Millions of square kilometers of the Earth’s surface is covered by forest fragments, and a quarter of remaining tropical forest has been fragmented. In Southeast Asia, about 650,000 ha of natural forests are fragmented per year. Fragmentation of old growth forests is considered to be the greatest th

  1. Effect of wildfires on the genetic microbial diversity in forest soils from Canary Islands (Spain

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    J. Rodríguez

    2013-05-01

    Full Text Available Wildfires produce several ecological and environmental impacts on the physical and chemical soil characteristics, as well as on the properties and dynamics of soil microbial populations. Microorganisms are good indicators of ecosystem function and sustainability and therefore the studies about the impact of fire on microbial communities is relevant to understand the role of fire in ecosystem functioning. Although several authors have provided data about total microbial biomass and activity in soils affected by fires, there is little information about the composition and evolution of soil microbial populations after the passage of fire. In this work the effect of wildfires on the genetic diversity of microbial populations in soils from the island of Tenerife (Canary Islands, Spain is studied. The final objective was to get information about the recovery of soil functionality after wildfires.

  2. Effects of Logging on the Genetic Diversity of Quercus tiaoloshanica Chun et Ko in a Tropical Montane Forest of Hainan Island, Southern China

    Institute of Scientific and Technical Information of China (English)

    Jian-Wei ZHENG; Shu-Qing AN; Lin CHEN; Xin LENG; Zhong-Sheng WANG; Hua-Jun XIANG

    2005-01-01

    Quercus tiaoloshanica Chun et Ko, which has a narrow range of distribution, is one of the important endemic species of the tropical montane rain forest on Hainan Island, southern China. Long-term logging and habitat destruction have resulted in population decline and distribution retreat of Q. tiaoloshanica. To determine the impact of logging on the genetic diversity of Q. tiaoloshanica, the authors investigated the genetic structures using amplified fragment length polymorphism markers in four regenerated stands after logging and in one unlogged stand. Compared with the unlogged stand, the effective number of alleles per locus dropped by 1.0% in selective logging stands and by 2.0% in clear logging stands,corresponding to reductions of 3.8% and 5.2%, respectively, in mean Nei's gene diversity and 2.9% and 3.5%, respectively, in mean Shannon diversity index. No substantial genetic erosion was detected in any of the regenerated stands owing to the high tree density and high heterogeneity of the Q. tiaoloshanica stands investigated. Meanwhile, there was no natural regeneration of the species observed in a Dacrydium pierrei Hickel plantation 700 m away from the regenerated stands, suggesting the limited ability of seed dispersal of Q. tiaoloshanica. Clear logging should be undertaken cautiously because the total number of plant species dropped by 15.2% in the clear-logged stands compared with the unlogged stand. To conserve the genetic diversity of this species, as well as the plant biodiversity of tropical forests, the habitats of Q. tiaoloshanica should be protected against exploitation in terms of agricultural or other forms of land use, and some mature trees should be preserved as seed sources to maintain an adequate regeneration base for this species in the management of logging.

  3. The conservation of diversity in forest trees

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    F. Thomas Ledig

    1988-01-01

    Deforestation, pollution, and climatic change threaten forest diversity all over the world. And because forests are the habitats for diverse organisms, the threat is extended to all the flora and fauna associated with forests, not only forest trees. In a worst case scenario, if the tropical forest in Latin America was reduced to the areas now set aside in parks and...

  4. Impacts of forest fragmentation on the mating system and genetic diversity of white spruce (Picea glauca) at the landscape level.

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    O'Connell, L M; Mosseler, A; Rajora, O P

    2006-12-01

    We studied the mating system of white spruce (Picea glauca) in a landscape fragmented by agriculture in northern Ontario, Canada. We sampled 23 stands that ranged in size from 1 to >500 trees isolated by 250-3000 m from the nearest other stand. Six polymorphic allozyme loci from four enzyme systems were used to genotype approximately 10 000 embryos from 104 families. We detected no allele frequency heterogeneity in the pollen pool among stands or families (Phi(FT)=-0.025). Overall, estimates of outcrossing were high (t(m)=94% and mean t(s)=91%) but significantly different from unity. Bi-parental inbreeding (t(m)-t(s)=3.2%) was low but significantly different from zero. Allozyme-based outcrossing estimates did not differ significantly among three stand-size classes (SSCs): small (large (> or =100 trees). The number of effective pollen donors was high in all SSCs, but was significantly lower in small stands (N(ep)=62.5) than in medium-sized and large stands (both N(ep)=143). The primary selfing rate was significantly higher in medium stands than in large stands. We found no significant difference in genetic diversity measures in the filial (seed) population among SSCs. Overall, these results indicate that white spruce stands in this fragmented landscape are resistant to genetic diversity losses, primarily through high pollen-mediated gene-flow and early selection against inbred embryos. We discuss the importance of using seed data, in conjunction with genetic data, to evaluate the impacts of fragmentation on natural populations.

  5. Genetic diversity patterns and functional traits of Bradyrhizobium strains associated with Pterocarpus officinalis Jacq. in Caribbean islands and Amazonian forest (French Guiana).

    Science.gov (United States)

    Le Roux, Christine; Muller, Félix; Bouvet, Jean-Marc; Dreyfus, Bernard; Béna, Gilles; Galiana, Antoine; Bâ, Amadou M

    2014-08-01

    Pterocarpus officinalis Jacq. is a legume tree native to the Caribbean islands and South America growing as a dominant species in swamp forests. To analyze (i) the genetic diversity and (ii) the symbiotic properties of its associated nitrogen-fixing soil bacteria, root nodules were collected from P. officinalis distributed in 16 forest sites of the Caribbean islands and French Guiana. The sequencing of the 16S-23S ribosomal RNA intergenic spacer region (ITS) showed that all bacteria belonged to the Bradyrhizobium genus. Bacteria isolated from insular zones showed very close sequence homologies with Bradyrhizobium genospecies V belonging to the Bradyrhizobium japonicum super-clade. By contrast, bacteria isolated from continental region displayed a larger genetic diversity and belonged to B. elkanii super-clade. Two strains from Puerto Rico and one from French Guiana were not related to any known sequence and could be defined as a new genospecies. Inoculation experiments did not show any host specificity of the Bradyrhizobium strains tested in terms of infectivity. However, homologous Bradyrhizobium sp. strain-P. officinalis provenance associations were more efficient in terms of nodule production, N acquisition, and growth than heterologous ones. The dominant status of P. officinalis in the islands may explain the lower bacterial diversity compared to that found in the continent where P. officinalis is associated with other leguminous tree species. The specificity in efficiency found between Bradyrhizobium strains and host tree provenances could be due to a coevolution process between both partners and needs to be taken in consideration in the framework of rehabilitation plantation programs.

  6. Genetic diversity of Metrodorea nigra (Rutaceae) from a small forest remnant in Brazil assessed with microsatellite markers.

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    Guidugli, M C; Ferreira-Ramos, R; de Sousa, A C B; Cidade, F W; Marconi, T G; Mestriner, M A; Groppo, M; Alzate-Marin, A L

    2012-01-09

    Metrodorea nigra (Rutaceae) is an endemic Brazilian tree of great ecological importance, frequently found in the submontane regions of ombrophilous dense and semideciduous forests. This tree is useful for reforesting degraded areas and the wood can be employed in construction. We developed 12 microsatellite markers from a genomic library enriched for GA/CA repeats, for this species. Polymorphisms were assessed in 40 trees of a highly fragmented population found in Cravinhos, State of São Paulo, in southeastern Brazil. Among the 12 loci, 8 were polymorphic and only one had fixed alleles in this population. The number of alleles per locus and expected heterozygosity ranged from 2 to 11 and from 0.190 to 0.889, respectively. These results revealed moderate levels of genetic variation in M. nigra population when compared to other tropical species. Additionally, transferability of the 12 primers was tested in seven other Brazilian Rutaceae tree species (endemics: M. stipularis, Galipea jasminiflora, Esenbeckia leiocarpa and non-endemics: E. febrifuga, E. grandiflora, Balfourodendron riedelianum, Zanthoxylum riedelianum). Transferability ranged among species, but at least 8 loci (~67%) amplified in M. stipularis, demonstrating a high potential for transferring microsatellite markers between species of the same genus in the Rutaceae family.

  7. Forest genetic resources to support global bioeconomy

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    Saša Orlović

    2015-01-01

    Full Text Available A biobased economy implies sustainable and effective use of the biomass. This includes new products from forestry. The sustainable production, use, consumption and waste management of biomass all contribute to a bioeconomy (The European Bioeconomy in 2030. In the context of bioeconomy the conservation of forest genetic resources assumes a key significance in overcoming global challenges such as climate change. Forests are expected to play a key role in climate change mitigation, but they will only be able to fulfil that role if the trees themselves are able to survive and adapt to changing climate conditions. Genetic diversity provides the fundamental basis for the evolution of forest tree species and for their adaptation to change. The enormous range of goods and services provided by trees and forests is both a function of and testimony to the genetic variability contained within them.  Conserving forest  genetic  resources  is  therefore  vital, as  they  constitute  a  unique  and  irreplaceable resource for the future, including for sustainable economic growth and progress and environmental adaption (The State of the Worlds Forest Genetic Resources 2014.Previous research of population characteristics and the effects of natural and artificial selection on the genetic structure of populations contribute to the conservation and enhancement of the gene pool of the native tree species. The balance model of the population genetic structure reveals the new properties of the populations and requires further investigations, especially of the relations of subpopulations, half-sib families and organisms and the effect of variable factors of the environment, on the exchange of genetic material within natural and cultural populations.Being of national and international significance, these resources require intensive protection and enhancement in situ and ex situ. In this paper a general introduction is given to conservation of forest genetic

  8. Genetic diversity and disease susceptibility.

    OpenAIRE

    Bodmer, W F

    1997-01-01

    The range of genetic diversity within human populations is enormous. Genetic susceptibility to common chronic disease is a significant part of this genetic diversity, which also includes a variety of rare clear-cut inherited diseases. Modern DNA-based genomic analysis can now routinely lead to the identification of genes involved in disease susceptibility, provides the basis for genetic counselling in affected families, and more widely for a genetically targeted approach to disease prevention...

  9. The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca).

    Science.gov (United States)

    Haag, T; Santos, A S; Sana, D A; Morato, R G; Cullen, L; Crawshaw, P G; De Angelo, C; Di Bitetti, M S; Salzano, F M; Eizirik, E

    2010-11-01

    Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large-scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars' ability to effectively disperse across the human-dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift. © 2010 Blackwell Publishing Ltd.

  10. Exploring genetic diversity, physiologic expression and carbon dynamics in longleaf pine: a new study installation at the Harrison Experimental Forest

    Science.gov (United States)

    John R. Butnor; Kurt H. Johnsen; C. Dana Nelson

    2012-01-01

    In 1960, an experiment was established on the Harrison Experimental Forest in southeast Mississippi to compare productivity and wood properties of planted longleaf (Pinus palustris), loblolly (Pinus taeda), and slash (Pinus elliotii) pines under different management intensities: cultivation, cultivation plus...

  11. Forest structure in low diversity tropical forests: a study of Hawaiian wet and dry forests

    Science.gov (United States)

    R. Ostertag; F. Inman-Narahari; S. Cordell; C.P. Giardina; L. Sack

    2014-01-01

    The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai‘i Island. We compared the species...

  12. Forest biological diversity interactions with resource utilization

    Science.gov (United States)

    S.T. Mok

    1992-01-01

    The most important forest resources of the Asia-Pacific region are the highly diverse rain forests. Utilization of the resource is a natural and inevitable consequence of the region's socio-economic development. The sustainable management and development of forest resources in the region can be achieved by implementing conservational forestry, which is based on...

  13. Adaptive genetic potential of coniferous forest tree species under climate change: implications for sustainable forest management

    Science.gov (United States)

    Mihai, Georgeta; Birsan, Marius-Victor; Teodosiu, Maria; Dumitrescu, Alexandru; Daia, Mihai; Mirancea, Ionel; Ivanov, Paula; Alin, Alexandru

    2017-04-01

    Mountain ecosystems are extremely vulnerable to climate change. The real potential for adaptation depends upon the existence of a wide genetic diversity in trees populations, upon the adaptive genetic variation, respectively. Genetic diversity offers the guarantee that forest species can survive, adapt and evolve under the influence of changing environmental conditions. The aim of this study is to evaluate the genetic diversity and adaptive genetic potential of two local species - Norway spruce and European silver fir - in the context of regional climate change. Based on data from a long-term provenance experiments network and climate variables spanning over more than 50 years, we have investigated the impact of climatic factors on growth performance and adaptation of tree species. Our results indicate that climatic and geographic factors significantly affect forest site productivity. Mean annual temperature and annual precipitation amount were found to be statistically significant explanatory variables. Combining the additive genetic model with the analysis of nuclear markers we obtained different images of the genetic structure of tree populations. As genetic indicators we used: gene frequencies, genetic diversity, genetic differentiation, genetic variance, plasticity. Spatial genetic analyses have allowed identifying the genetic centers holding high genetic diversity which will be valuable sources of gene able to buffer the negative effects of future climate change. Correlations between the marginal populations and in the optimal vegetation, between the level of genetic diversity and ecosystem stability, will allow the assessment of future risks arising from current genetic structure. Therefore, the strategies for sustainable forest management have to rely on the adaptive genetic variation and local adaptation of the valuable genetic resources. This work was realized within the framework of the project GENCLIM (Evaluating the adaptive potential of the main

  14. Genetics and Forest Seed Handling

    DEFF Research Database (Denmark)

    Schmidt, Lars Holger

    2016-01-01

    High genetic quality seed is obtained from seed sources that match the planting site, have a good outcrossing rate, and are superior in some desirable characters. Non-degraded natural forests and plantations may be used as untested seed sources, which can sometimes be managed to promote outbreedi...

  15. Genetics of Forest Seed Handling

    DEFF Research Database (Denmark)

    Schmidt, Lars Holger

    2016-01-01

    High genetic quality seed is obtained from seed sources that match the planting site, have a good outcrossing rate, and are superior in some desirable characters. Non-degraded natural forests and plantations may be used as untested seed sources, which can sometimes be managed to promote outbreeding...

  16. Forest structure in low-diversity tropical forests: a study of Hawaiian wet and dry forests.

    Science.gov (United States)

    Ostertag, Rebecca; Inman-Narahari, Faith; Cordell, Susan; Giardina, Christian P; Sack, Lawren

    2014-01-01

    The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS) methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai'i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai'i forests were characterized by low species richness and very high relative dominance. The two Hawai'i forests were floristically distinct, yet similar in species richness (15 vs. 21 species) and stem density (3078 vs. 3486/ha). While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5->50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai'i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15-1182 species), six-fold variation in mean annual rainfall (835-5272 mm yr(-1)) and 1.8-fold variation in mean annual temperature (16.0-28.4°C). Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological theory for

  17. In situ conservation and landscape genetics in forest species

    Directory of Open Access Journals (Sweden)

    Martín L.M.

    2012-03-01

    Full Text Available Conservation of forest genetic resources is essential for sustaining the environmental and productive values of forests. One of the environmental values is the conservation of the diversity that is assessed through the amount of genetic diversity stored by forests, their structure and dynamics. The current need for forest conservation and management has driven a rapid expansion of landscape genetics discipline that combines tools from molecular genetics, landscape ecology and spatial statistics and is decisive for improving not only ecological knowledge but also for properly managing population genetic resources. The objective of this study is to show the way to establish the safeguard of genetic diversity through this approach using the results obtained in sweet chestnut (Castanea sativa Mill. that has provided a better understanding on the species genetic resources. In this respect, we will show how the information provided by different types of molecular markers (genomic and genic offer more accurate indication on the distribution of the genetic diversity among and within populations assuming different evolutionary drivers.

  18. Conservation of forest genetic resources in the United States.

    Science.gov (United States)

    B. St. Clair; S. Lipow; K. Vance-Borland; R. Johnson

    2007-01-01

    Conservation of genetic diversity is recognized as an important requirement of sustainable forest management. Gene conservation activities include in situ conservation of native stands in reserves and ex situ conservation in seed banks, genetic tests, seed and breeding orchards, and other plantations of known identity. We present an example from Oregon and Washington...

  19. Forest genetic monitoring: an overview of concepts and definitions.

    Science.gov (United States)

    Fussi, Barbara; Westergren, Marjana; Aravanopoulos, Filippos; Baier, Roland; Kavaliauskas, Darius; Finzgar, Domen; Alizoti, Paraskevi; Bozic, Gregor; Avramidou, Evangelia; Konnert, Monika; Kraigher, Hojka

    2016-08-01

    Safeguarding sustainability of forest ecosystems with their habitat variability and all their functions is of highest priority. Therefore, the long-term adaptability of forest ecosystems to a changing environment must be secured, e.g., through sustainable forest management. High adaptability is based on biological variation starting at the genetic level. Thus, the ultimate goal of the Convention on Biological Diversity (CBD) to halt the ongoing erosion of biological variation is of utmost importance for forest ecosystem functioning and sustainability. Monitoring of biological diversity over time is needed to detect changes that threaten these biological resources. Genetic variation, as an integral part of biological diversity, needs special attention, and its monitoring can ensure its effective conservation. We compare forest genetic monitoring to other biodiversity monitoring concepts. Forest genetic monitoring (FGM) enables early detection of potentially harmful changes of forest adaptability before these appear at higher biodiversity levels (e.g., species or ecosystem diversity) and can improve the sustainability of applied forest management practices and direct further research. Theoretical genetic monitoring concepts developed up to now need to be evaluated before being implemented on a national and international scale. This article provides an overview of FGM concepts and definitions, discusses their advantages and disadvantages, and provides a flow chart of the steps needed for the optimization and implementation of FGM. FGM is an important module of biodiversity monitoring, and we define an effective FGM scheme as consisting of an assessment of a forest population's capacity to survive, reproduce, and persist under rapid environmental changes on a long-term scale.

  20. Modeling Forest Structure and Vascular Plant Diversity in Piedmont Forests

    Science.gov (United States)

    Hakkenberg, C.

    2014-12-01

    When the interacting stressors of climate change and land cover/land use change (LCLUC) overwhelm ecosystem resilience to environmental and climatic variability, forest ecosystems are at increased risk of regime shifts and hyperdynamism in process rates. To meet the growing range of novel biotic and environmental stressors on human-impacted ecosystems, the maintenance of taxonomic diversity and functional redundancy in metacommunities has been proposed as a risk spreading measure ensuring that species critical to landscape ecosystem functioning are available for recruitment as local systems respond to novel conditions. This research is the first in a multi-part study to establish a dynamic, predictive model of the spatio-temporal dynamics of vascular plant diversity in North Carolina Piedmont mixed forests using remotely sensed data inputs. While remote sensing technologies are optimally suited to monitor LCLUC over large areas, direct approaches to the remote measurement of plant diversity remain a challenge. This study tests the efficacy of predicting indices of vascular plant diversity using remotely derived measures of forest structural heterogeneity from aerial LiDAR and high spatial resolution broadband optical imagery in addition to derived topo-environmental variables. Diversity distribution modelling of this sort is predicated upon the idea that environmental filtering of dispersing species help define fine-scale (permeable) environmental envelopes within which biotic structural and compositional factors drive competitive interactions that, in addition to background stochasticity, determine fine-scale alpha diversity. Results reveal that over a range of Piedmont forest communities, increasing structural complexity is positively correlated with measures of plant diversity, though the nature of this relationship varies by environmental conditions and community type. The diversity distribution model is parameterized and cross-validated using three high

  1. Genetic diversity in Entamoeba histolytica

    Indian Academy of Sciences (India)

    C Graham Clark; Mehreen Zaki; Ibne Karim Md Ali

    2002-11-01

    Genetic diversity within Entamoeba histolytica led to the re-description of the species 10 years ago. However, more recent investigation has revealed significant diversity within the re-defined species. Both protein-coding and non-coding sequences show variability, but the common feature in all cases is the presence of short tandem repeats of varying length and sequence. The ability to identify strains of E. histolytica may lead to insights into the population structure and epidemiology of the organism.

  2. The role of glacial cycles in promoting genetic diversity in the Neotropics: the case of cloud forests during the Last Glacial Maximum

    OpenAIRE

    Ramírez-Barahona, Santiago; Eguiarte, Luis E.

    2013-01-01

    The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contras...

  3. Sex and the single squirrel: a genetic view of forest management in the Pacific Northwest.

    Science.gov (United States)

    Sally. Duncan

    2003-01-01

    Forest management throughout the world is producing simplified forests. There is growing concern that these forests maintain neither complete vertebrate communities nor conditions favorable to maintenance of genetic diversity of those vertebrate populations that do find habitat in simply structured stands. Genetics is increasingly being used as a basis for management...

  4. European genetic conservation strategies of forest trees in the context of currently running climate change

    NARCIS (Netherlands)

    Vries, de S.M.G.

    2015-01-01

    The diversity of forests, at the level of species and at the level of genetic diversity within species, is an important resource for Europe. Over the past several decades countries have made efforts to conserve the diversity of tree species and genetic diversity. However, there was no harmonised app

  5. Genetic diversity in Trichomonas vaginalis.

    Science.gov (United States)

    Meade, John C; Carlton, Jane M

    2013-09-01

    Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations.

  6. Forest structure in low-diversity tropical forests: a study of Hawaiian wet and dry forests.

    Directory of Open Access Journals (Sweden)

    Rebecca Ostertag

    Full Text Available The potential influence of diversity on ecosystem structure and function remains a topic of significant debate, especially for tropical forests where diversity can range widely. We used Center for Tropical Forest Science (CTFS methodology to establish forest dynamics plots in montane wet forest and lowland dry forest on Hawai'i Island. We compared the species diversity, tree density, basal area, biomass, and size class distributions between the two forest types. We then examined these variables across tropical forests within the CTFS network. Consistent with other island forests, the Hawai'i forests were characterized by low species richness and very high relative dominance. The two Hawai'i forests were floristically distinct, yet similar in species richness (15 vs. 21 species and stem density (3078 vs. 3486/ha. While these forests were selected for their low invasive species cover relative to surrounding forests, both forests averaged 5->50% invasive species cover; ongoing removal will be necessary to reduce or prevent competitive impacts, especially from woody species. The montane wet forest had much larger trees, resulting in eightfold higher basal area and above-ground biomass. Across the CTFS network, the Hawaiian montane wet forest was similar to other tropical forests with respect to diameter distributions, density, and aboveground biomass, while the Hawai'i lowland dry forest was similar in density to tropical forests with much higher diversity. These findings suggest that forest structural variables can be similar across tropical forests independently of species richness. The inclusion of low-diversity Pacific Island forests in the CTFS network provides an ∼80-fold range in species richness (15-1182 species, six-fold variation in mean annual rainfall (835-5272 mm yr(-1 and 1.8-fold variation in mean annual temperature (16.0-28.4°C. Thus, the Hawaiian forest plots expand the global forest plot network to enable testing of ecological

  7. Global genetic diversity of Aedes aegypti.

    Science.gov (United States)

    Gloria-Soria, Andrea; Ayala, Diego; Bheecarry, Ambicadutt; Calderon-Arguedas, Olger; Chadee, Dave D; Chiappero, Marina; Coetzee, Maureen; Elahee, Khouaildi Bin; Fernandez-Salas, Ildefonso; Kamal, Hany A; Kamgang, Basile; Khater, Emad I M; Kramer, Laura D; Kramer, Vicki; Lopez-Solis, Alma; Lutomiah, Joel; Martins, Ademir; Micieli, Maria Victoria; Paupy, Christophe; Ponlawat, Alongkot; Rahola, Nil; Rasheed, Syed Basit; Richardson, Joshua B; Saleh, Amag A; Sanchez-Casas, Rosa Maria; Seixas, Gonçalo; Sousa, Carla A; Tabachnick, Walter J; Troyo, Adriana; Powell, Jeffrey R

    2016-11-01

    Mosquitoes, especially Aedes aegypti, are becoming important models for studying invasion biology. We characterized genetic variation at 12 microsatellite loci in 79 populations of Ae. aegypti from 30 countries in six continents, and used them to infer historical and modern patterns of invasion. Our results support the two subspecies Ae. aegypti formosus and Ae. aegypti aegypti as genetically distinct units. Ae. aegypti aegypti populations outside Africa are derived from ancestral African populations and are monophyletic. The two subspecies co-occur in both East Africa (Kenya) and West Africa (Senegal). In rural/forest settings (Rabai District of Kenya), the two subspecies remain genetically distinct, whereas in urban settings, they introgress freely. Populations outside Africa are highly genetically structured likely due to a combination of recent founder effects, discrete discontinuous habitats and low migration rates. Ancestral populations in sub-Saharan Africa are less genetically structured, as are the populations in Asia. Introduction of Ae. aegypti to the New World coinciding with trans-Atlantic shipping in the 16th to 18th centuries was followed by its introduction to Asia in the late 19th century from the New World or from now extinct populations in the Mediterranean Basin. Aedes mascarensis is a genetically distinct sister species to Ae. aegypti s.l. This study provides a reference database of genetic diversity that can be used to determine the likely origin of new introductions that occur regularly for this invasive species. The genetic uniqueness of many populations and regions has important implications for attempts to control Ae. aegypti, especially for the methods using genetic modification of populations. © 2016 John Wiley & Sons Ltd.

  8. Diversity and production in an Afromontane Forest

    Directory of Open Access Journals (Sweden)

    Klaus v. Gadow

    2016-07-01

    Full Text Available Background This contribution evaluates the effect of forest structure and tree species diversity on plot productivity and individual tree growth in the unique Knysna forests in Southern Africa using mapped tree data from an observational study that has been re-measured over a period of 40 years. Methods The effects of tree species diversity and forest structure on tree growth and forest production are evaluated on three levels of resolution: a the forest community (canopy, sub-canopy species, b the subplots (number of trees per ha, skewness of the diameter distribution, diameter coefficient of variation and c the immediate neighborhood of selected reference trees (“Mingling”, “Dominance”, Aggregation” and “Size Variation”. Results An analysis of the community level identified two distinct clusters, one including dominant/canopy species with the highest growth rates and a greater variation of growth, and another cluster which includes the remaining subcanopy species which have a smaller maximum size and lower rates of growth. The area-based structure variables on plot level have a highly significant effect on total basal area growth. However, the effects of forest density and species richness on productivity were not straight forward. Maximum basal area production of about 0.75 m2/ha/year is achieved at medium levels of richness (around 20 species per ha and medium levels of density (around 30 m2/ha basal area using percentile regression estimates. The relative “Dominance” of a selected reference tree had a highly significant effect on individual tree growth on all investigated species. Other neighbourhood structure variables were only occasionally significant or not significant at all. Conclusion This contribution presents a new theoretical framework for analysing natural forests that includes community, plot and neighborhood variables of forest structure and diversity, and a first specific analysis of the structure and

  9. Genetic diversity of Przewalski's gazelle using noninvasive DNA and ...

    African Journals Online (AJOL)

    Cynthia

    2015-04-01

    Apr 1, 2015 ... 1Institute of Forestry Ecology, Environment and Protection and the Key Laboratory of Forest Ecology and ... In order to understand the genetic structure and diversity of ... important for the purposes of conservation management, especially for the identification of evolutionary significant ..... Biological.

  10. Genetic diversity Study of Dioscoreas Using Morphological Traits ...

    African Journals Online (AJOL)

    Prof. Ogunji

    major yam species are tropical plants and do not grow well below 200 C. ... cayenesis - rotundata complex were collected in. West Africa and ... tropical forest with mean annual rainfall of. 1,200mm, mean ..... Genetic structure and diversity in ...

  11. Application of SRAP in the genetic diversity of Tricholoma matsutake ...

    African Journals Online (AJOL)

    GREGORY

    2010-09-20

    Sep 20, 2010 ... The study firstly applied SRAP technique into genetic diversity of T. matsutake. A total of ... widely in coniferous trees, especially Pinus densiflora forests, and ..... Lian CL, Oishi R, Miyashita N, Nara K, Nakaya H, Wu B, Zhou Z,.

  12. Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

    Institute of Scientific and Technical Information of China (English)

    Chadaporn SENAKUN; Suchitra CHANGTRAGOON; Pairot PRAMUAL; Preecha PRATHEPHA

    2011-01-01

    Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study,the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximately 3% of genetic variation partitioned among populations. This may indicate that the populations sampled were recently part of a continuous population. A tree constructed using the unweighted pair group method with arithmetic average, based on Nei's genetic distance, divided the populations into three groups. This separation was consistent with the altitudinal zonation of the populations,thus indicating that altitude might play a significant role in the genetic structure of S. obtusa. Areas of high genetic diversity were identified which could be considered priorities for conservation.

  13. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

    Science.gov (United States)

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-02-10

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community.

  14. Genetic diversity of Kenyan native oyster mushroom (Pleurotus).

    Science.gov (United States)

    Otieno, Ojwang D; Onyango, Calvin; Onguso, Justus Mungare; Matasyoh, Lexa G; Wanjala, Bramwel W; Wamalwa, Mark; Harvey, Jagger J W

    2015-01-01

    Members of the genus Pleurotus, also commonly known as oyster mushroom, are well known for their socioeconomic and biotechnological potentials. Despite being one of the most important edible fungi, the scarce information about the genetic diversity of the species in natural populations has limited their sustainable utilization. A total of 71 isolates of Pleurotus species were collected from three natural populations: 25 isolates were obtained from Kakamega forest, 34 isolates from Arabuko Sokoke forest and 12 isolates from Mount Kenya forest. Amplified fragment length polymorphism (AFLP) was applied to thirteen isolates of locally grown Pleurotus species obtained from laboratory samples using five primer pair combinations. AFLP markers and internal transcribed spacer (ITS) sequences of the ribosomal DNA were used to estimate the genetic diversity and evaluate phylogenetic relationships, respectively, among and within populations. The five primer pair combinations generated 293 polymorphic loci across the 84 isolates. The mean genetic diversity among the populations was 0.25 with the population from Arabuko Sokoke having higher (0.27) diversity estimates compared to Mount Kenya population (0.24). Diversity between the isolates from the natural population (0.25) and commercial cultivars (0.24) did not differ significantly. However, diversity was greater within (89%; P > 0.001) populations than among populations. Homology search analysis against the GenBank database using 16 rDNA ITS sequences randomly selected from the two clades of AFLP dendrogram revealed three mushroom species: P. djamor, P. floridanus and P. sapidus; the three mushrooms form part of the diversity of Pleurotus species in Kenya. The broad diversity within the Kenyan Pleurotus species suggests the possibility of obtaining native strains suitable for commercial cultivation.

  15. Global biological diversity, forests and ecosystem approach

    Directory of Open Access Journals (Sweden)

    Corona P

    2010-07-01

    Full Text Available Recent international reports and a paper published on Science stresses the lack of evidence about the reduction in the rate of biodiversity decline as expected as a consequence of political agreements on global environment. This decline is of particular concern not only with respect to the intrinsic value of the nature as such but also because it involves the reduction or loss of ecosystem services. This issue is distinctively relevant for forest ecosystems. The Ecosystem Approach proposed by the United Nations Convention on Biological Diversity might be a strategy to reverse the negative trend, promoting a fair conservation and sustainable use of natural resources on an operational level.

  16. Microbial diversity - insights from population genetics

    NARCIS (Netherlands)

    Mes, T.H.M.

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, Ne, is one of the parameters that determines population genetic

  17. Genetic diversity in Populus nigra plantations from west of Iran

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-11-01

    Full Text Available In order to adopt strategies for forest conservation and development,it is necessary to estimate the amount and distribution of genetic diversity in existing populations of poplar in Iran. In this study, the genetic diversity between eight stands of Populus nigra established in Kermanshah province was evaluated on the basis of molecular and morphological markers. To amplify microsatellite loci (WPMS09, WPMS16 and WPMS18, DNA extraction from young and fresh leaveswas done. Various conditions of the PCR assay were examined and to evaluate the morphological variation of the morphological characters leaves (consist of 19 traits were measured. In addition, height growth was measured, to evaluate the growth function of the stands in homogeneous conditions. Genetic diversity in termof polymorphic loci was 0%, because three investigated microsatellite loci were monomorphic. The total number of alleles for 3 microsatellite loci was 6 (na = 2, ne = 2, heo = 1, hee = 0.51. Genetic identity based on Nei was 100%, so genetic distance was 0%. The whole sampled trees represented the same thus the genotype. No significant differences between the mean values of all morphological characters and height growth were revealed. Observed genetic similarity gave indication that same ramets had been selected to plant in poplar plantation established in Kermanshah province.These results suggest the need for an initial evaluation of the genetic diversity in selected ramets for planting in plantation to avoid repetition.

  18. Genetic diversity in Populus nigra plantations from west of Iran

    Directory of Open Access Journals (Sweden)

    Afrooz Alimohamadi

    2012-12-01

    Full Text Available In order to adopt strategies for forest conservation and development, it is necessary to estimate the amount and distribution of genetic diversity in existing populations of poplar in Iran. In this study, the genetic diversity between eight stands of Populus nigra established in Kermanshah province was evaluated on the basis of molecular and morphological markers. To amplify microsatellite loci (WPMS09, WPMS16 and WPMS18, DNA extraction from young and fresh leaveswas done. Various conditions of the PCR assay were examined and to evaluate the morphological variation of the morphological characters leaves (consist of 19 traits were measured. In addition, height growth was measured, to evaluate the growth function of the stands in homogeneous conditions. Genetic diversity in term of polymorphic loci was 0%, because three investigated microsatellite loci were monomorphic. The total number of alleles for 3 microsatellite loci was 6 (na = 2, ne = 2, heo = 1, hee = 0.51. Genetic identity based on Nei was 100%, so genetic distance was 0%. The whole sampled trees represented the same thus the genotype. No significant differences between the mean values of all morphological characters and height growth were revealed. Observed genetic similarity gave indication that same ramets had been selected to plant in poplar plantation established in Kermanshah province. These results suggest the need for an initial evaluation of the genetic diversity in selected ramets for planting in plantation to avoid repetition.  

  19. Study of Siberian forest genetic resources

    Directory of Open Access Journals (Sweden)

    L. I. Milyutin

    2016-06-01

    Full Text Available Forest genetic resources are the aggregate of genofonds of native and cultivar populations of forest woody plants, valuable really or potential for specific territory (A brief dictionary… 2014. Forest genetic resources are studied in practice in most cases on example of forest-forming woody plants. It is necessary to consider of study of these resources in two positions: taxonomic and geographic. Forest forming coniferous species are studied best of all from the taxonomic point of view taking into account biodiversity. Genetic polymorphism is studied most in detail with such species as Pinus sylvestris, Pinus sibirica, Larix sibirica, Larix sukaczevii, Picea obovata, Abies sibirica. Populations of Larix gmelinii, Larix cajanderi, Picea ajanensis are studied considerable worse. Materials about genetic polymorphism of forest forming foliage species – representative of genera Betula and Populus are absent. Caryological polymorphism is studied sufficiently well in all Siberian conifer species. It should be noted especially attached to examination of this problem, that individuals with B-chromosome were discovered first by gymnosperms as an example Picea obovata. Discovery in Siberia of triploid asp deserve special attention. Geographic variability is shown most broadly in the investigations of Pinus sylvestris, Pinus sibirica, Larix sibirica. These investigations were conducted both in natural populations and in provenance trials. Such investigations of another conifer and foliage species either are shown by separate fragments or are absent at all Geographic variability is shown in a large measure in the operative forest seed sources regionalization. Numerous investigations directed to the analysis of morphological variability are conducted by all forest forming species in the first place by conifers. Questions of hereditary determination of either signs remain in this problem. Similar questions concern the variability of other signs

  20. The paradox of forest fragmentation genetics

    Science.gov (United States)

    Andrea T. Kramer; Jennifer L. Ison; Mary V. Ashley; Henry F. Howe

    2008-01-01

    Theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce. We argue that population genetics theory may be misapplied in light of ecological realities that, when recognized, require scrutiny of underlying evolutionary assumptions. One ecological reality is...

  1. Utilization and transfer of forest genetic resources

    DEFF Research Database (Denmark)

    Koskela, Jarkko; Vinceti, Barbara; Dvorak, William

    2014-01-01

    Over the last 200 years, genetic resources of forest trees have been increasingly transferred, within and outside of species’ native distribution ranges, for forestry and for research and development (R&D). Transferred germplasm has been deployed to grow trees for numerous purposes, ranging from ...

  2. Forest Genetic Resources Conservation and Management

    DEFF Research Database (Denmark)

    Ukendt, FAO; Ukendt, DFSC; Ukendt, ICRAF

    FAO, IPGRI/SAFORGEN, DFSCand ICRAF have cooperated on the compilation of17 booklets on the state of Forest Genetic Resources for thecountries listed below. When ordering your book please remember to write the country required on the email. Benin, Burkina Faso, Cote d\\Ivoire, Ethiopia, Gambia...

  3. Species diversity and area-relationships in Danish beech forests

    NARCIS (Netherlands)

    Lawesson, J.E.; Blust, de G.; Grashof, C.; Firbanks, L.; Honnay, O.; Hermy, M.; Hobitz, P.; Jensen, L.M.

    1998-01-01

    The vascular flora of 62 Danish beech forests of eastern Jutland ranging in size from 1-445 ha, was investigated for species-area relations. Species richness reflecting total diversity, forest diversity, and of different habitat groups, were corrected for non-linearity by means of a log-log power fu

  4. Genetic diversity and population structure in Meconopsis ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-05-24

    May 24, 2010 ... including the populations distributed in same location together in every group. ... Key words: Meconopsis quintuplinervia Regel, genetic diversity, random amplified ..... in its original center, and Banma population located in ...

  5. Molecular genetics of human pigmentation diversity

    National Research Council Canada - National Science Library

    Sturm, Richard A

    2009-01-01

    The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between...

  6. Evolution and genetic diversity of Theileria.

    Science.gov (United States)

    Sivakumar, Thillaiampalam; Hayashida, Kyoko; Sugimoto, Chihiro; Yokoyama, Naoaki

    2014-10-01

    Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development.

  7. Genetic diversity of 11 European pig breeds

    NARCIS (Netherlands)

    Lavall, G.; Iannuccelli, N.; Legault, C.; Milan, D.; Groenen, M.A.M.; Andersson, L.; Fredholm, M.; Geldermann, H.; Foulley, J.L.; Chevalet, C.; Ollivier, L.

    2000-01-01

    A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosi

  8. COMPARITIVE GENETIC DIVERSITY ANALYSIS OF OAT (Avena ...

    African Journals Online (AJOL)

    knsccf

    Equivalence was appraised between phenotypic and molecular markers (ISSR) to analyze the genetic diversity of 20 ... Country of origin. Pedigree ... explain between and within geographical variation and granting ..... JM (2008). Development of PCR-based SCAR and ... Genetic. Resources and Crop Evolution, 56:465–480.

  9. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    OpenAIRE

    Cardoso Márcio Z; Quek Swee-Peck; Albuquerque de Moura Priscila; Kronforst Marcus R

    2011-01-01

    Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on po...

  10. Structural and genetic diversity in antibody repertoires from diverse species.

    Science.gov (United States)

    de los Rios, Miguel; Criscitiello, Michael F; Smider, Vaughn V

    2015-08-01

    The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.

  11. Microbial diversity--insights from population genetics.

    Science.gov (United States)

    Mes, Ted H M

    2008-01-01

    Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

  12. Diversity and carbon storage across the tropical forest biome

    Science.gov (United States)

    Sullivan, Martin J. P.; Talbot, Joey; Lewis, Simon L.; Phillips, Oliver L.; Qie, Lan; Begne, Serge K.; Chave, Jerôme; Cuni-Sanchez, Aida; Hubau, Wannes; Lopez-Gonzalez, Gabriela; Miles, Lera; Monteagudo-Mendoza, Abel; Sonké, Bonaventure; Sunderland, Terry; Ter Steege, Hans; White, Lee J. T.; Affum-Baffoe, Kofi; Aiba, Shin-Ichiro; de Almeida, Everton Cristo; de Oliveira, Edmar Almeida; Alvarez-Loayza, Patricia; Dávila, Esteban Álvarez; Andrade, Ana; Aragão, Luiz E. O. C.; Ashton, Peter; Aymard C., Gerardo A.; Baker, Timothy R.; Balinga, Michael; Banin, Lindsay F.; Baraloto, Christopher; Bastin, Jean-Francois; Berry, Nicholas; Bogaert, Jan; Bonal, Damien; Bongers, Frans; Brienen, Roel; Camargo, José Luís C.; Cerón, Carlos; Moscoso, Victor Chama; Chezeaux, Eric; Clark, Connie J.; Pacheco, Álvaro Cogollo; Comiskey, James A.; Valverde, Fernando Cornejo; Coronado, Eurídice N. Honorio; Dargie, Greta; Davies, Stuart J.; de Canniere, Charles; Djuikouo K., Marie Noel; Doucet, Jean-Louis; Erwin, Terry L.; Espejo, Javier Silva; Ewango, Corneille E. N.; Fauset, Sophie; Feldpausch, Ted R.; Herrera, Rafael; Gilpin, Martin; Gloor, Emanuel; Hall, Jefferson S.; Harris, David J.; Hart, Terese B.; Kartawinata, Kuswata; Kho, Lip Khoon; Kitayama, Kanehiro; Laurance, Susan G. W.; Laurance, William F.; Leal, Miguel E.; Lovejoy, Thomas; Lovett, Jon C.; Lukasu, Faustin Mpanya; Makana, Jean-Remy; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Junior, Ben Hur Marimon; Marshall, Andrew R.; Morandi, Paulo S.; Mukendi, John Tshibamba; Mukinzi, Jaques; Nilus, Reuben; Vargas, Percy Núñez; Camacho, Nadir C. Pallqui; Pardo, Guido; Peña-Claros, Marielos; Pétronelli, Pascal; Pickavance, Georgia C.; Poulsen, Axel Dalberg; Poulsen, John R.; Primack, Richard B.; Priyadi, Hari; Quesada, Carlos A.; Reitsma, Jan; Réjou-Méchain, Maxime; Restrepo, Zorayda; Rutishauser, Ervan; Salim, Kamariah Abu; Salomão, Rafael P.; Samsoedin, Ismayadi; Sheil, Douglas; Sierra, Rodrigo; Silveira, Marcos; Slik, J. W. Ferry; Steel, Lisa; Taedoumg, Hermann; Tan, Sylvester; Terborgh, John W.; Thomas, Sean C.; Toledo, Marisol; Umunay, Peter M.; Gamarra, Luis Valenzuela; Vieira, Ima Célia Guimarães; Vos, Vincent A.; Wang, Ophelia; Willcock, Simon; Zemagho, Lise

    2017-01-01

    Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity.

  13. Diversity and carbon storage across the tropical forest biome

    Science.gov (United States)

    Sullivan, Martin J. P.; Talbot, Joey; Lewis, Simon L.; Phillips, Oliver L.; Qie, Lan; Begne, Serge K.; Chave, Jerôme; Cuni-Sanchez, Aida; Hubau, Wannes; Lopez-Gonzalez, Gabriela; Miles, Lera; Monteagudo-Mendoza, Abel; Sonké, Bonaventure; Sunderland, Terry; ter Steege, Hans; White, Lee J. T.; Affum-Baffoe, Kofi; Aiba, Shin-ichiro; de Almeida, Everton Cristo; de Oliveira, Edmar Almeida; Alvarez-Loayza, Patricia; Dávila, Esteban Álvarez; Andrade, Ana; Aragão, Luiz E. O. C.; Ashton, Peter; Aymard C., Gerardo A.; Baker, Timothy R.; Balinga, Michael; Banin, Lindsay F.; Baraloto, Christopher; Bastin, Jean-Francois; Berry, Nicholas; Bogaert, Jan; Bonal, Damien; Bongers, Frans; Brienen, Roel; Camargo, José Luís C.; Cerón, Carlos; Moscoso, Victor Chama; Chezeaux, Eric; Clark, Connie J.; Pacheco, Álvaro Cogollo; Comiskey, James A.; Valverde, Fernando Cornejo; Coronado, Eurídice N. Honorio; Dargie, Greta; Davies, Stuart J.; De Canniere, Charles; Djuikouo K., Marie Noel; Doucet, Jean-Louis; Erwin, Terry L.; Espejo, Javier Silva; Ewango, Corneille E. N.; Fauset, Sophie; Feldpausch, Ted R.; Herrera, Rafael; Gilpin, Martin; Gloor, Emanuel; Hall, Jefferson S.; Harris, David J.; Hart, Terese B.; Kartawinata, Kuswata; Kho, Lip Khoon; Kitayama, Kanehiro; Laurance, Susan G. W.; Laurance, William F.; Leal, Miguel E.; Lovejoy, Thomas; Lovett, Jon C.; Lukasu, Faustin Mpanya; Makana, Jean-Remy; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Junior, Ben Hur Marimon; Marshall, Andrew R.; Morandi, Paulo S.; Mukendi, John Tshibamba; Mukinzi, Jaques; Nilus, Reuben; Vargas, Percy Núñez; Camacho, Nadir C. Pallqui; Pardo, Guido; Peña-Claros, Marielos; Pétronelli, Pascal; Pickavance, Georgia C.; Poulsen, Axel Dalberg; Poulsen, John R.; Primack, Richard B.; Priyadi, Hari; Quesada, Carlos A.; Reitsma, Jan; Réjou-Méchain, Maxime; Restrepo, Zorayda; Rutishauser, Ervan; Salim, Kamariah Abu; Salomão, Rafael P.; Samsoedin, Ismayadi; Sheil, Douglas; Sierra, Rodrigo; Silveira, Marcos; Slik, J. W. Ferry; Steel, Lisa; Taedoumg, Hermann; Tan, Sylvester; Terborgh, John W.; Thomas, Sean C.; Toledo, Marisol; Umunay, Peter M.; Gamarra, Luis Valenzuela; Vieira, Ima Célia Guimarães; Vos, Vincent A.; Wang, Ophelia; Willcock, Simon; Zemagho, Lise

    2017-01-01

    Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity. PMID:28094794

  14. Resilience of Amazon forests emerges from plant trait diversity

    Science.gov (United States)

    Sakschewski, Boris; von Bloh, Werner; Boit, Alice; Poorter, Lourens; Peña-Claros, Marielos; Heinke, Jens; Joshi, Jasmin; Thonicke, Kirsten

    2016-11-01

    Climate change threatens ecosystems worldwide, yet their potential future resilience remains largely unquantified. In recent years many studies have shown that biodiversity, and in particular functional diversity, can enhance ecosystem resilience by providing a higher response diversity. So far these insights have been mostly neglected in large-scale projections of ecosystem responses to climate change. Here we show that plant trait diversity, as a key component of functional diversity, can have a strikingly positive effect on the Amazon forests' biomass under future climate change. Using a terrestrial biogeochemical model that simulates diverse forest communities on the basis of individual tree growth, we show that plant trait diversity may enable the Amazon forests to adjust to new climate conditions via a process of ecological sorting, protecting the Amazon's carbon sink function. Therefore, plant trait diversity, and biodiversity in general, should be considered in large-scale ecosystem projections and be included as an integral part of climate change research and policy.

  15. Banking on the future: progress, challenges and opportunities for the genetic conservation of forest trees

    Science.gov (United States)

    Kevin M. Potter; Robert M. Jetton; Andrew Bower; Douglass F. Jacobs; Gary Man; Valerie D. Hipkins; Murphy Westwood

    2017-01-01

    Genetic diversity provides the essential basis for the adaptation and resilience of tree species to environmental stress and change. The genetic conservation of tree species is an urgent global necessity as forest conversion and fragmentation continue apace, damaging insects and pathogens are transported between continents, and climate change alters local habitat...

  16. Pathogenic potential, genetic diversity, and population structure of Escherichia coli strains isolated from a forest-dominated watershed (Comox Lake) in British Columbia, Canada.

    Science.gov (United States)

    Chandran, Abhirosh; Mazumder, Asit

    2015-03-01

    Escherichia coli isolates (n = 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs): stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae and the adherence factor (EAF) gene (enteropathogenic E. coli [EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). The only genes detected were eae and stx2, which were carried by 37.69% (n = 248) of the isolates. Only eae was harbored by 26.74% (n = 176) of the isolates, representing potential atypical EPEC strains, while only stx2 was detected in 10.33% (n = 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both the stx2 and eae genes, representing potential EHEC strains. The prevalence of VGs (eae or stx2) was significantly (P < 0.0001) higher in the fall season, and multiple genes (eae plus stx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658 E. coli isolates identified 335 unique fingerprints, with an overall Shannon diversity (H') index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure of E. coli fluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenic E. coli strains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water.

  17. Soil Effects on Forest Structure and Diversity in a Moist and a Dry Tropical Forest

    NARCIS (Netherlands)

    Peña-Claros, M.; Poorter, L.; Alarcon, A.; Blate, G.; Choque, U.; Fredericksen, T.S.; Justiniano, J.; Leaño, C.; Licona, J.C.; Pariona, W.; Putz, F.E.; Quevedo, L.; Toledo, M.

    2012-01-01

    Soil characteristics are important drivers of variation in wet tropical forest structure and diversity, but few studies have evaluated these relationships in drier forest types. Using tree and soil data from 48 and 32 1 ha plots, respectively, in a Bolivian moist and dry forest, we asked how soil co

  18. Nephronophthisis: A Genetically Diverse Ciliopathy

    Directory of Open Access Journals (Sweden)

    Roslyn J. Simms

    2011-01-01

    Full Text Available Nephronophthisis (NPHP is an autosomal recessive cystic kidney disease and a leading genetic cause of established renal failure (ERF in children and young adults. Early presenting symptoms in children with NPHP include polyuria, nocturia, or secondary enuresis, pointing to a urinary concentrating defect. Renal ultrasound typically shows normal kidney size with increased echogenicity and corticomedullary cysts. Importantly, NPHP is associated with extra renal manifestations in 10–15% of patients. The most frequent extrarenal association is retinal degeneration, leading to blindness. Increasingly, molecular genetic testing is being utilised to diagnose NPHP and avoid the need for a renal biopsy. In this paper, we discuss the latest understanding in the molecular and cellular pathogenesis of NPHP. We suggest an appropriate clinical management plan and screening programme for individuals with NPHP and their families.

  19. Allozymes Genetic Diversity of Quercus mongolica Fisch in China

    Institute of Scientific and Technical Information of China (English)

    LI Wenying; GU Wanchun

    2006-01-01

    A gel electrophoresis method was used to study the genetic diversity of 8 Quercus mongolica populations throughout its range in China.Eleven of 21 loci from 13 enzymes assayed were polymorphic.Q.mongolica maintained low level of genetic variation compared with the average Quercus species.At the species level,: the mean number of alleles per locus (A) was 1.905, the percentage of polymorphic loci (P) was 52.38%, the observed heterozygosity (He) was 0.092 and the expected heterozygosity (He) was 0.099.At the population level, the estimates were A =1.421, P =28.976%, Ho= 0.088, He =0.085.Genetic differentiation (Gst was high among populations, it was 0.107.According to the UPGMA cluster analysis based on the genetic distance, 4 populations located in northeast and 2 populations in southwest of the geographical distribution are classified into 2 subgroups, but there was no clear relationship between genetic distance and geographic distance among populations.The low level of genetic diversity of Q.mongolica might be related to the long-term exploitation as economic tree species in history are comparatively seriously disturbed and damaged by human beings, and most of the existing stands are secondary forests.

  20. Eco-geographic Distribution and Microcenters of Genetic Diversity in ...

    African Journals Online (AJOL)

    Eco-geographic Distribution and Microcenters of Genetic Diversity in Faba Bean ... Ethiopia is considered an important center of secondary diversity for both ... the microcenter of genetic diversity for both crops may be located in the southern ...

  1. Understorey bird abundance and diversity before and after a forest ...

    African Journals Online (AJOL)

    Comparisons of Shannon-. Wiener diversities were performed using a t-test described by Hutcheson (1970). .... HUtcHeson, K. 1970. A test for comparing ... Bird use of burned and unburned coniferous forest during winter. Wilson Bulletin 111: ...

  2. Maintaining forest diversity in a changing climate: A geophysical approach

    Science.gov (United States)

    Mark Anderson; Nels Johnson; Scott Bearer

    2014-01-01

    Forest conservationists need a method to conserve the maximum amount of biological diversity while allowing species and communities to rearrange in response to a continually changing climate. Here, we develop such an approach for northeastern North America. First we characterize and categorize forest blocks based on their geology, landforms, and elevation zones. Next,...

  3. Forest climbing plants of West Africa: diversity, ecology and management

    NARCIS (Netherlands)

    Bongers, F.J.J.M.; Parren, M.P.E.; Traoré, D.

    2005-01-01

    Climbing plants, including lianas, represent a fascinating component of the ecology of tropical forests. This book focuses on the climbing plants of West African forests. Based on original research, it presents information on the flora (including a checklist), diversity (with overviews at several le

  4. Chemical analyses, antibacterial activity and genetic diversity ...

    African Journals Online (AJOL)

    SAM

    2014-06-25

    Jun 25, 2014 ... Key words: Citrus, genetic diversity, ISSR markers, chemical analyses, antibacterial. ... ment of DNA based marker systems has advanced our ... Total acidity of the juices was determined by titration method as ... Greek compressed C. sinensis. 37 163 ..... flavonoids have a large spectrum of biological activity.

  5. Genetic diversity among sorghum landraces and polymorphism ...

    African Journals Online (AJOL)

    1 Institute of Environment and Agricultural Research (INERA), BP 910 Bobo Dioulasso, ... This investigation was undertaken to study the genetic diversity among local ... resources could develop new and durable production systems. The biological basis of world food security .... Two control panel DNA samples were used in.

  6. Does genetic diversity predict health in humans?

    Directory of Open Access Journals (Sweden)

    Hanne C Lie

    Full Text Available Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC, has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d(2 at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d(2 at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d(2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d(2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations.

  7. Genetic Diversity of the Ring-Tailed Lemur (Lemur catta) in South-Central Madagascar.

    Science.gov (United States)

    Clarke, Tara A; Gray, Olivia; Gould, Lisa; Burrell, Andrew S

    2015-01-01

    Madagascar's lemurs, now deemed the most endangered group of mammals, represent the highest primate conservation priority in the world. Due to anthropogenic disturbances, an estimated 10% of Malagasy forest cover remains. The endangered Lemur catta is endemic to the southern regions of Madagascar and now occupies primarily fragmented forest habitats. We examined the influence of habitat fragmentation and isolation on the genetic diversity of L. catta across 3 different forest fragments in south-central Madagascar. Our analysis revealed moderate levels of genetic diversity. Genetic differentiation among the sites ranged from 0.05 to 0.11. These data suggest that the L. catta populations within south-central Madagascar have not yet lost significant genetic variation. However, due to ongoing anthropogenic threats faced by ring-tailed lemurs, continued conservation and research initiatives are imperative for long-term viability of the species. © 2015 S. Karger AG, Basel.

  8. Drivers of bacterial beta diversity in two temperate forests

    NARCIS (Netherlands)

    Wang, Xugao; Li, Hui; Bezemer, T.Martijn; Hao, Zhanqing

    2016-01-01

    Although the consequences of changes in microbial diversity have received increasing attention, our understanding of processes that drive spatial variation in microbial diversity remains limited. In this study, we sampled bacterial communities in early and late successional temperate forests in Nort

  9. Genetic diversity of eleven European pig breeds

    Directory of Open Access Journals (Sweden)

    Foulley Jean-Louis

    2000-03-01

    Full Text Available Abstract A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies generally agreed with Hardy-Weinberg expectations, apart from the German Landrace and Schwäbisch-Hällisches breeds, which showed significantly reduced heterozygosity. Breed differentiation was significant as shown by the high among-breed fixation index (overall FST = 0.27, and confirmed by the clustering based on the genetic distances between individuals, which grouped essentially all individuals in 11 clusters corresponding to the 11 breeds. The genetic distances between breeds were first used to construct phylogenetic trees. The trees indicated that a genetic drift model might explain the divergence of the two German breeds, but no reliable phylogeny could be inferred among the remaining breeds. The same distances were also used to measure the global diversity of the set of breeds considered, and to evaluate the marginal loss of diversity attached to each breed. In that respect, the French Basque breed appeared to be the most "unique" in the set considered. This study, which remains to be extended to a larger set of European breeds, indicates that using genetic distances between breeds of farm animals in a classical taxonomic approach may not give clear resolution, but points to their usefulness in a prospective evaluation of diversity.

  10. Kitobo Forest of Kenya, a unique hotspot of herpetofaunal diversity

    Directory of Open Access Journals (Sweden)

    Patrick K. Malonza

    2011-12-01

    Full Text Available Herpetologically, the remoteness of Kitobo forest in south-eastern Kenya has partly contributed to it remaining virtually un-explored until 2007. Three surveys were conducted in December 2007, December 2009 and April 2010 aimed at generating a comprehensive list of the forest amphibians and reptiles. Using largely timed-species count method, 13 species of amphibians representing eight families and 32 reptiles belonging to 11 families were recorded. Overall species diversity was highest during the 2007 sampling. The richness and abundance of amphibians was highest during the April 2010 sampling period when the amount of rainfall was also highest. The results of species accumulation curves of the three sampling periods did not plateau demonstrating that more species occur in this forest. Pressure on this forest fragment from the adjacent local people is high which in addition to the annual floods threatens its long-term survival. For example the distribution and abundance of some forest associated species such as the tree frogs Leptopelis flavomaculatus and Hyperolius puncticulatus appear to fluctuate with flood events and may decline in future. Considering the forest associated herpetofanua recorded, Kitobo forest is zoogeographically assignable to the East African coastal forest biodiversity hotspot. The documentation of high species richness and diversity in this small forest fragment strongly highlight its biodiversity importance and place it among the most important sites for the conservation of reptiles and amphibians in Kenya.

  11. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems

    Science.gov (United States)

    Wang, Jun-Tao; Zheng, Yuan-Ming; Hu, Hang-Wei; Li, Jing; Zhang, Li-Mei; Chen, Bao-Dong; Chen, Wei-Ping; He, Ji-Zheng

    2016-01-01

    The belowground soil prokaryotic community plays a cardinal role in sustaining the stability and functions of forest ecosystems. Yet, the nature of how soil prokaryotic diversity co-varies with aboveground plant diversity along a latitudinal gradient remains elusive. By establishing three hundred 400-m2 quadrats from tropical rainforest to boreal forest in a large-scale parallel study on both belowground soil prokaryote and aboveground tree and herb communities, we found that soil prokaryotic diversity couples with the diversity of herbs rather than trees. The diversity of prokaryotes and herbs responds similarly to environmental factors along the latitudinal gradient. These findings revealed that herbs provide a good predictor of belowground biodiversity in forest ecosystems, and provide new perspective on the aboveground and belowground interactions in forest ecosystems.

  12. Genetic improvement of forest tree species

    Directory of Open Access Journals (Sweden)

    Teotônio Francisco Assis

    2011-01-01

    Full Text Available Brazilian forestry sector is considered one of the most developed in the world, being the base for important industrialsegments which use wood as raw material. Tree breeding has played an important role on improving the competitiveness ofBrazilian forestry-based companies, especially for its positive reflexes on increasing adaptation, forestry productivity and woodquality. In spite of the importance of other forest trees for the economy, such as Schizolobium, Araucaria, Populus and Hevea, themain genera under genetic improvement in the country are Eucalyptus, Pinus, Acacia and Tectona. They are used by industries likepulp and paper, siderurgy, tannin, chips for exportation and lumber, constituting an important source of revenues for the Brazilian’seconomy, besides their positive social and environmental impacts. This paper presents a generic approach to genetic improvementaspects of these four major genera currently undergoing breeding in Brazil.

  13. [Application of genetic diversity in the researches on rodents].

    Science.gov (United States)

    Liu, Zhu; Yang, Chun-Wen; Xu, Yan-Chun; Jin, Zhi-Min; Ma, Jian-Zhang

    2014-02-01

    Genetic diversity is the base of the species diversity and ecosystem diversity, and also the foundation for biological evolution and species differentiation. Furthermore, genetic diversity is important evidence for evaluation of biological resources of nature. The genetic diversity data from a wide variety of rodents have many complex applications. We summarized the application of rodent prevention, the origin and differentiation including evolutionary history of rodents, the potential adaptation of rodents, the dynamics of population and regulatory mechanisms, and the conservation biology of rodents. Researches in the future should focus on the systematic study on the relationships between population dynamics and genetic diversity, and long-term monitoring of genetic diversity of rodents.

  14. Conservation of forest genetic resources and sustainable forest management in Europe

    NARCIS (Netherlands)

    Koskela, J.; Vries, de S.M.G.; Gil, L.; Mátyás, C.; Rusanen, M.; Paule, L.

    2004-01-01

    Considerable efforts have been made to enhance conservation of forest genetic resources and to promote sustainable forest management in Europe over the past decade. The need to enhance genetic conservation emerged from a concern about the impacts of environmental pollution and genetic erosion on for

  15. Conservation of forest genetic resources and sustainable forest management in Europe

    NARCIS (Netherlands)

    Koskela, J.; Vries, de S.M.G.; Gil, L.; Mátyás, C.; Rusanen, M.; Paule, L.

    2004-01-01

    Considerable efforts have been made to enhance conservation of forest genetic resources and to promote sustainable forest management in Europe over the past decade. The need to enhance genetic conservation emerged from a concern about the impacts of environmental pollution and genetic erosion on

  16. Deforestation and plant diversity of Madagascar's littoral forests.

    Science.gov (United States)

    Consiglio, Trisha; Schatz, George E; McPherson, Gordon; Lowry, Porter P; Rabenantoandro, Johny; Rogers, Zachary S; Rabevohitra, Raymond; Rabehevitra, David

    2006-12-01

    Few studies have attempted to quantify the reduction or document the floristic composition of forests in Madagascar. Thus, we focused specifically on deforestation and plant diversity in Madagascar's eastern littoral community. We used a data set of approximately 13,500 specimen records compiled from both historical and contemporary collections resulting from recent intensive inventory efforts to enumerate total plant species richness and to analyze the degree of endemism within littoral forests. Change in littoral forest cover from original to current extent was estimated using geographical information systems tools, remote sensing data (satellite imagery and low-elevation digital photography), and environmental data layers. Of the original littoral forest only 10.3% remains in the form of small forest parcels, and only 1.5% of these remaining fragments are included within the existing protected-areas network. Additionally, approximately 13% of Madagascar's total native flora has been recorded from these forests that originally occupied land surface, and over 25% of the 1535 plant species known from littoral forests are endemic to this community. Given the ongoing pressure from human settlement along Madagascar's eastern coast, protection of the remaining forest fragments is critical for their survival. Fifteen of the largest intact littoral forest fragments we identified, collectively representing 41.5% of remaining littoral forest, are among priority sites recommended to the government of Madagascar for plant conservation and incorporation into the protected-areas network.

  17. Forest microbiome: diversity, complexity and dynamics.

    Science.gov (United States)

    Baldrian, Petr

    2016-11-16

    Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.

  18. Managing genetic diversity and society needs

    Directory of Open Access Journals (Sweden)

    Arthur da Silva Mariante

    2008-07-01

    Full Text Available Most livestock are not indigenous to Brazil. Several animal species were considered domesticated in the pre-colonial period, since the indigenous people manage them as would be typical of European livestock production. For over 500 years there have been periodic introductions resulting in the wide range of genetic diversity that for centuries supported domestic animal production in the country. Even though these naturalized breeds have acquired adaptive traits after centuries of natural selection, they have been gradually replaced by exotic breeds, to such an extent, that today they are in danger of extinction To avoid further loss of this important genetic material, in 1983 Embrapa Genetic Resources and Biotechnology decided to include conservation of animal genetic resources among its priorities. In this paper we describe the effort to genetically characterize these populations, as a tool to ensure their genetic variability. To effectively save the threatened local breeds of livestock it is important to find a niche market for each one, reinserting them in production systems. They have to be utilized in order to be conserved. And there is no doubt that due to their adaptive traits, the Brazilian local breeds of livestock can play an important role in animal production, to meet society needs.

  19. 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...... species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central....../eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost...

  20. Genetic Diversity of the Black Mangrove Avicennia germinans (L. Stearn in Northwestern Mexico

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    Olivia Millán-Aguilar

    2016-09-01

    Full Text Available Mangrove forests of Mexico have been threatened by the effects of anthropogenic activities during the last decades, mostly related to aquaculture, agriculture, livestock and urban development. Genetic diversity and fine-scale genetic structure of two generations of the black mangrove Avicennia germinans (L. Stearn were investigated in perturbed and preserved sites from three lagoon systems in Sinaloa, Mexico. Genetic diversity and overall genetic structure were similar between perturbed and preserved sites. However, lower levels of fine-scale spatial genetic structure were observed in two of the younger (sapling generations. We attribute this to differences in local dynamics of each lagoon system, their status of conservation and levels of fragmentation. Also, low connectivity and the effects of disturbance could restrict the movement of pollinators and seed dispersal capabilities, resulting in low levels of genetic diversity and signs of inbreeding. Perturbed populations of A. germinans may play an important role in in situ conservation of this complex ecosystem.

  1. Genetic diversity in Tunisian horse breeds

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    B. Jemmali

    2017-06-01

    Full Text Available This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49, 7.35 (0.54, 6.3 (0.44, and 6 (0.38 for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03 in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02 in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05 and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

  2. Opposing Responses of Bird Functional Diversity to Vegetation Structural Diversity in Wet and Dry Forest.

    Science.gov (United States)

    Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian

    2016-01-01

    Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation

  3. Structural diversity of forest communities on Baihuashan Mountain,Beijing

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The structural diversity of forests on Baihuashan Mountain,Beijing,was surveyed by a plotless method combined with branch and leaf coverage estimation in the different layers.New structural indices were constructed,calculated and compared among different communities.On the basis of previous work,structural diversity of forest communities at the stand level was described by a vertical complexity index and a horizontal heterogeneity index.From a correlational analysis among the new indices and other commonly used biodiversity indices,we concluded that the new indices are closely related to a tree height inequality index and the Shannon-Wiener index of the tree and shrub layer,which indicated that the new indices were good at indicating structural diversity in the different forests on Baihuashan Mountain.The results show that,in natural forests,structural diversity of pioneer communities is much lower than in late successive communities.In plantations,structural diversity is determined by the stage of development and tree species.Tending would increase horizontal heterogeneity and decrease vertical complexity.

  4. Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest

    Science.gov (United States)

    Chaverri, Gloriana; Garin, Inazio; Alberdi, Antton; Jimenez, Lide; Castillo-Salazar, Cristian; Aihartza, Joxerra

    2016-01-01

    Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied, particularly for taxa that are difficult to sample such as bats. Aiming to estimate the amount of cryptic diversity among bats of a Neotropical montane cloud forest in Talamanca Range—south-east Central America—, we performed a 15-night sampling campaign, which resulted in 90 captured bats belonging to 8 species. We sequenced their mitochondrial cytochrome c oxidase subunit I (COI) and screened their inter- and intraspecific genetic variation. Phylogenetic relations with conspecifics and closely related species from other geographic regions were established using Maximum Likelihood and Bayesian inference methods, as well as median-joining haplotype networks. Mitochondrial lineages highly divergent from hitherto characterized populations (> 9% COI dissimilarity) were found in Myotis oxyotus and Hylonycteris underwoodi. Sturnira burtonlimi and M. keaysi also showed distinct mitochondrial structure with sibling species and/or populations. These results suggest that mountains in the region hold a high degree of endemicity potential that has previously been ignored in bats. They also warn of the high extinction risk montane bats may be facing due to climatic change, particularly in isolated mountain systems like Talamanca Range. PMID:27706168

  5. Forest genetic resources in Serbia: State and recommendations for improvement in this area

    Directory of Open Access Journals (Sweden)

    Šijačić-Nikolić Mirjana

    2014-01-01

    Full Text Available Forest genetic resources, which represent genetic diversity contained in the thousands of forest tree species, take a significant place in total biodiversity of Serbia. The forest ecosystems of Serbia include about 250 indigenous tree species which, according to geographical-floral elements, belong to the Middle-European, Pontic and Mediterranean element. Within the available gene pool, special attention should be addressed to wild fruit tree species and those species which are relict, endemic, rare and endangered according to the IUCN categorization. The regulatory basis for conservation and directed utilization of forest genetic resources in Serbia can be found in the strategic and legal acts in the field of environmental protection, nature conservation and forestry. Previous activities in the conservation of forest genetic resources are insufficient, whereby the level of their endangerment is continuously increasing as a result of deforestation and climate change. This situation requires a clear definition of a national strategy of conservation and directed utilization of forest genetic resources in Serbia, as a basis for planning activities in this area based on best practices.

  6. Diversity-Carbon Flux Relationships in a Northwest Forest

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    Rachael E. Kelm

    2011-12-01

    Full Text Available While aboveground biomass and forest productivity can vary over abiotic gradients (e.g., temperature and moisture gradients, biotic factors such as biodiversity and tree species stand dominance can also strongly influence biomass accumulation. In this study we use a permanent plot network to assess variability in aboveground carbon (C flux in forest tree annual aboveground biomass increment (ABI, tree aboveground net primary productivity (ANPPtree, and net soil CO2 efflux in relation to diversity of coniferous, deciduous, and a nitrogen (N-fixing tree species (Alnus rubra. Four major findings arose: (1 overstory species richness and indices of diversity explained between one third and half of all variation in measured aboveground C flux, and diversity indices were the most robust models predicting measured aboveground C flux; (2 trends suggested decreases in annual tree biomass increment C with increasing stand dominance for four of the five most abundant tree species; (3 the presence of an N-fixing tree species (A. rubra was not related to changes in aboveground C flux, was negatively related to soil CO2 efflux, and showed only a weak negative relationship with aboveground C pools; and (4 stands with higher overstory richness and diversity typically had higher soil CO2 efflux. Interestingly, presence of the N-fixing species was not correlated with soil inorganic N pools, and inorganic N pools were not correlated with any C flux or pool measure. We also did not detect any strong patterns between forest tree diversity and C pools, suggesting potential balancing of increased C flux both into and out of diverse forest stands. These data highlight variability in second-growth forests that may have implications for overstory community drivers of C dynamics.

  7. Genetic Diversity of Koala Retroviral Envelopes

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    Wenqin Xu

    2015-03-01

    Full Text Available Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process.

  8. Genetic Diversity of Koala Retroviral Envelopes

    Science.gov (United States)

    Xu, Wenqin; Gorman, Kristen; Santiago, Jan Clement; Kluska, Kristen; Eiden, Maribeth V.

    2015-01-01

    Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A) were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process. PMID:25789509

  9. Genetic diversity in aspen and its relation to arthropod abundance.

    Science.gov (United States)

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2014-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen.

  10. Genetic diversity in populations of Acrocomia aculeata (Arecaceae) in the northern region of Minas Gerais, Brazil.

    Science.gov (United States)

    Oliveira, D A; Melo Júnior, A F; Brandão, M M; Rodrigues, L A; Menezes, E V; Ferreira, P R B

    2012-03-08

    Macaúba (Acrocomia aculeata) is a palm of economic importance, widely distributed in natural forests from Mexico to Uruguay. We analyzed the genetic diversity of populations of macaúba (A. aculeata) in the northern region of the State of Minas Gerais, Brazil. Young leaves from 10 macaúba individuals encompassing 49 genotypes of macaúba were collected from Montes Claros, Itacambira, Brasília de Minas, Mirabela, and Grão Mogol. After extraction and amplification of samples, the amplified fragments were separated by electrophoresis. We found high levels of genetic diversity within the populations. Genetic diversity indices were high, except in the Itacambira and Mirabela populations. Results show that Mirabela and Itacambira populations can require conservation strategies because they present lower values of genetic diversity.

  11. Tropical forests are not flat: how mountains affect herbivore diversity.

    Science.gov (United States)

    Rodríguez-Castañeda, Genoveva; Dyer, Lee A; Brehm, Gunnar; Connahs, Heidi; Forkner, Rebecca E; Walla, Thomas R

    2010-11-01

    Ecologists debate whether tropical insect diversity is better explained by higher plant diversity or by host plant species specialization. However, plant-herbivore studies are primarily based in lowland rainforests (RF) thus excluding topographical effects on biodiversity. We examined turnover in Eois (Geometridae) communities across elevation by studying elevational transects in Costa Rica and Ecuador. We found four distinct Eois communities existing across the elevational gradients. Herbivore diversity was highest in montane forests (MF), whereas host plant diversity was highest in lowland RF. This was correlated with higher specialization and species richness of Eois/host plant species we found in MF. Based on these relationships, Neotropical Eois richness was estimated to range from 313 (only lowland RF considered) to 2034 (considering variation with elevation). We conclude that tropical herbivore diversity and diet breadth covary significantly with elevation and urge the inclusion of montane ecosystems in host specialization and arthropod diversity estimates. © 2010 Blackwell Publishing Ltd/CNRS.

  12. Arthropod diversity in a tropical forest

    DEFF Research Database (Denmark)

    Basset, Yves; Cizek, Lukas; Cuénoud, Philippe

    2012-01-01

    Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic...

  13. Functional diversity changes during tropical forest succession.

    NARCIS (Netherlands)

    Lohbeck, M.W.M.; Poorter, L.; Paz, H.; Breugel, van M.; Martinez-Ramos, M.; Bongers, F.

    2012-01-01

    Functional diversity (FD) ‘those components of biodiversity that influence how an ecosystem operates or functions’ is a promising tool to assess the effect of biodiversity loss on ecosystem functioning. FD has received ample theoretical attention, but empirical studies are limited. We evaluate chang

  14. The influence of compositional and structural diversity on forest productivity

    Science.gov (United States)

    James N. Long; John D. Shaw

    2010-01-01

    Data from ~1500 ponderosa pine (Pinus ponderosa C. Lawson) stands in the western United States were used to examine the potential influence of compositional and structural diversity on forest productivity. Relative density, height and site quality were combined in a conceptually sound expression of the relationship between growth and growing stock for ponderosa pine-...

  15. Disturbance, diversity and distributions in Central African rain forest

    NARCIS (Netherlands)

    Gemerden, van B.S.

    2004-01-01

    The aim of this study is to gain insight in the impact of human land use on plant community composition, diversity and levels of endemism in Central African rain forest. Human disturbance in this region is causing large-scale habitat degradation. The two most widespread forms of land use are selecti

  16. Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

    Directory of Open Access Journals (Sweden)

    Cardoso Márcio Z

    2011-01-01

    Full Text Available Abstract Background Brazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of two Heliconius butterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on population connectivity in butterflies with home-range behavior. Results We generated microsatellite, AFLP and mtDNA sequence data for 136 Heliconius erato specimens from eight collecting locations and 146 H. melpomene specimens from seven locations. Population genetic analyses of the data revealed high levels of genetic diversity in H. erato relative to H. melpomene, widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance. Conclusions These results are consistent with the hypothesis that the extensive habitat fragmentation along Brazil's Atlantic Forest has reduced dispersal of Heliconius butterflies among neighboring habitat patches. The results also lend support to the observation that fine-scale population genetic structure may be common in Heliconius. If such population structure also exists independent of human activity, and has been common over the evolutionary history of Heliconius butterflies, it may have contributed to the evolution of wing pattern diversity in the genus.

  17. Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes.

    Science.gov (United States)

    Nazareno, Alison G; Jump, Alistair S

    2012-06-01

    Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.

  18. Forest management type influences diversity and community composition of soil fungi across temperate forest ecosystems

    Directory of Open Access Journals (Sweden)

    Kezia eGoldmann

    2015-11-01

    Full Text Available Fungal communities have been shown to be highly sensitive towards shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L., with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L. or spruce (Picea abies Karst. which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure.We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal OTU richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera.This study extends our knowledge

  19. Genetic diversity of Ehrlichia canis in Brazil.

    Science.gov (United States)

    Aguiar, D M; Zhang, X; Melo, A L T; Pacheco, T A; Meneses, A M C; Zanutto, M S; Horta, M C; Santarém, V A; Camargo, L M A; McBride, J W; Labruna, M B

    2013-06-28

    Canine monocytic ehrlichiosis is a highly prevalent disease in Brazil, where the genetic diversity of Ehrlichia canis remains undefined. In this study, we used the TRP36 gene to examine the genetic diversity of E. canis strains from naturally infected dogs residing in five distinct geographic regions in Brazil. E. canis DNA was detected in 82/126 (65%) dogs by dsb-specific PCR and E. canis was isolated in cell culture from 13 dogs. Sequences obtained from dsb genes amplified from the isolates were identical to the US E. canis strain. An extended molecular characterization based on the TRP36 gene identified two major genogroups based on differences among eight isolates. Isolates with tandem repeat amino acid sequence (TEDSVSAPA) identical to the previously reported TRP36 sequence were found in the midwest, northeast and southeast regions of Brazil, and classified into the US genogroup. A novel Brazilian genotype with a different tandem repeat sequence (ASVVPEAE) was also identified in midwest, northern and southern regions. Similarity in the N-terminal sequence of a US genogroup member with the Brazilian genogroup suggested that genomic recombination between the two genogroups may have occurred. Other subtypes within the Brazilian genogroup were also identified using C-terminal amino acid divergence. We identified two distinct major Brazilian genogroups and several subtypes based on analysis of TRP36, and such information will be useful for further genotyping and possible associations with disease severity, understanding of the genetic and antigenic variability of E. canis, and for developing strain-specific vaccines and diagnostic methods based on TRP36.

  20. Conservation of Genetic Diversity in Culture Plants

    Directory of Open Access Journals (Sweden)

    MAXIM A.

    2010-08-01

    Full Text Available The most important international document relating to the conservation of biodiversity is one adopted by theUN in Rio de Janeiro (1992 that "Convention on Biodiversity". Based on this agreement, the EU has taken a series ofmeasures to reduce genetic erosion in agriculture, which grew with the expansion of industrialized agriculture.Throughout its existence, mankind has used some 10,000 growing plant species. According to FAO statistics, today,90% of food production is ensured by some 120 growing plant species. In addition to drastic reduction in specificdiversity, the advent of industrialized agriculture has generated a process of strong genetic erosion. Old varieties andlocal varieties of crops have mostly been affected, in favour of "modern" varieties. Landraces are characterized by highheterogenity. They have the advantage of being much better adapted to biotic and abiotic stress conditions (diseases,pests, drought, low in nutrients, etc. and have excellent taste qualities, which can justify a higher price recovery thancommercial varieties. Thanks to these features, these crops need small inputs, which correspond to the concept ofsustainable development. Landraces are an invaluable genetic potential for obtaining new varieties of plants and are bestsuited for crop cultivation in ecological systems, becoming more common. Also, for long term food security in thecontext of global warming, rich genetic diversity will be require. “In situ” and “ex situ” conservation are the two majorstrategies used in the conservation of plant genetic resources. There is a fundamental difference between these twostrategies: “ex situ” conservation involves sampling, transfer and storage of a particular species population away fromthe original location, while “in situ” conservation (in their natural habitat implies that the varieties of interest,management and monitoring their place of origin takes place in the community to which they belong. These

  1. Floristic diversity analysis along a fragmentation gradients: a case study of beech forests in the Molisean Appenines (southern Italy

    Directory of Open Access Journals (Sweden)

    Frate L

    2011-11-01

    Full Text Available The process of fragmentation of natural habitats is increasing exponentially worldwide and represents one of the foremost threats to biological diversity. Forest fragmentation is considered to heavily affect the demographic and genetic structure of forest plant populations. Habitat fragmentation is a landscape process occurring when areas of continuous habitat are broken into smaller and discontinuous patches. In this paper we analyzed the effects of fragmentation on vascular plant diversity of Fagus sylvatica forest in central Italy (habitat of Community interest -92/43/ECC- “Appenine beech forests with Taxus and Ilex” - cod. 9210*. First, by integrating five parameters that describe beech forest patches structure (patch area, perimeter, shape index, corea area, euclidean nearest neighbor we identified three levels of fragmentation: high, medium and absent. Then the vascular plants of each level of fragmentation were sampled following a random stratified design. The diversity of vascular plant species was analyzed considering two species groups: all sampled species and “diagnostic” species of the habitat 9210* (sensu Directive 92/43/ECC. We compared the biodiversity patterns of the different fragmentation levels by using rarefaction curves and Rényi’s profiles. We also tested the significance of the founded differences by a bootstrapping procedure. The diversity pattern of the two species groups (diagnostics and all species showed two opposite trends. As the diversity of the entire pool of species increased on fragmented beech forests the diversity of the diagnostic group decreased. The differences between diversity values of high and low fragmentation levels resulted significant. Our results emphasize the existence of two diagnostic species: Cardamine kitaibelii and Paris quadrifolia that are indicators of not fragmented beech forests. Additionally the diversity pattern of the diagnostics species allow us to propose them as

  2. Arenavirus genetic diversity and its biological implications.

    Science.gov (United States)

    Emonet, Sebastien F; de la Torre, Juan C; Domingo, Esteban; Sevilla, Noemí

    2009-07-01

    The Arenaviridae family currently comprises 22 viral species, each of them associated with a rodent species. This viral family is important both as tractable experimental model systems to study acute and persistent infections and as clinically important human pathogens. Arenaviruses are enveloped viruses with a bi-segmented negative-strand RNA genome. The interaction with the cellular receptor and subsequent entry into the host cell differs between Old World and New World arenavirus that use alpha-dystoglycan or human transferring receptor 1, respectively, as main receptors. The recent development of reverse genetic systems for several arenaviruses has facilitated progress in understanding the molecular biology and cell biology of this viral family, as well as opening new approaches for the development of novel strategies to combat human pathogenic arenaviruses. On the other hand, increased availability of genetic data has allowed more detailed studies on the phylogeny and evolution of arenaviruses. As with other riboviruses, arenaviruses exist as viral quasispecies, which allow virus adaptation to rapidly changing environments. The large number of different arenavirus host reservoirs and great genetic diversity among virus species provide the bases for the emergence of new arenaviruses potentially pathogenic for humans.

  3. Molecular diversity and genetic relationships in Secale

    Indian Academy of Sciences (India)

    E. SANTOS; M. MATOS; P. SILVA; A. M. FIGUEIRAS; C. BENITO; O. PINTO-CARNIDE

    2016-06-01

    The objective of this study was to quantify the molecular diversity and to determine the genetic relationships amongSecalespp. and among cultivars ofSecale cerealeusing RAPDs, ISSRs and sequence analysis of six exons ofScMATE1gene.Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDsand 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primersgenerated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further,69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of theScMATE1gene also demonstrated a high genetic variability that subsists inSecalegenus. One difference observed in exon 1 sequencesfromS. vaviloviiseems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs,ISSRs and exons ofScMATE1gene were similar.S. ancestrale ,S. kuprijanoviiandS. cerealewere grouped in the same clusterandS. segetalewas in another cluster.S. vaviloviishowed evidences of not being clearly an isolate species and having greatintraspecific difference

  4. The silent threat of low genetic diversity

    Science.gov (United States)

    Hunter, Margaret E.

    2013-01-01

    Across the Caribbean, protected coastal waters have served as primary feeding and breeding grounds for the endangered Antillean manatee. Unfortunately, these same coastal waters are also a popular “habitat” for humans. In the past, the overlap between human and manatee habitat allowed for manatee hunting and threatened the survival of these gentle marine mammals. Today, however, threats are much more inadvertent and are often related to coastal development, degraded habitats and boat strikes. In the state of Florida, decades of research on the species’ biological needs have helped conservationists address threats to its survival. For example, low wake zones and boater education have protected manatees from boat strikes, and many of their critical winter refuges are now protected. The Florida population has grown steadily, thus increasing from approximately 1,200 in 1991 to more than 5,000 in 2010. It is conceivable that in Florida manatees may one day be reclassified as “threatened” rather than “endangered.” Yet, in other parts of the Caribbean, threats still loom. This includes small, isolated manatee populations found on islands that can be more susceptible to extinction and lack of genetic diversity. To ensure the species’ long-term viability, scientists have turned their sights to the overall population dynamics of manatees throughout the Caribbean. Molecular genetics has provided new insights into long-term threats the species faces. Fortunately, the emerging field of conservation genetics provides managers with tools and strategies for protecting the species’ long-term viability.

  5. Accounting for a Diverse Forest Ownership Structure in Projections of Forest Sustainability Indicators

    Directory of Open Access Journals (Sweden)

    Jeannette Eggers

    2015-11-01

    Full Text Available In this study, we assessed the effect of a diverse ownership structure with different management strategies within and between owner categories in long-term projections of economic, ecological and social forest sustainability indicators, representing important ecosystem services, for two contrasting Swedish municipalities. This was done by comparing two scenarios: one where the diversity of management strategies was accounted for (Diverse and one where it was not (Simple. The Diverse scenario resulted in a 14% lower total harvested volume for the 100 year period compared to the Simple scenario, which resulted in a higher growing stock and a more favorable development of the ecological indicators. The higher proportion of sparse forests and the lower proportion of clear-felled sites made the Diverse scenario more appropriate for delivering access to common outdoor recreation activities, while the Simple scenario projected more job opportunities. Differences between the scenarios were considerable already in the medium term (after 20 years of simulation. Our results highlight the importance of accounting for the variety of management strategies employed by forest owners in medium- to long-term projections of the development of forest sustainability indicators.

  6. Assessment of Genetic diversity in mutant cowpea lines using ...

    African Journals Online (AJOL)

    FKOLADE

    2016-11-09

    Nov 9, 2016 ... option of NTSYS, a rooted tree was also generated from the .... Dellarporta SF, Wood J, Hicks JB (1983). ... genetic diversity in Pigeon Pea (Cajanus sp). ... diversity in somatic mutants of grape (Vitis vinifera) cultivar Italia.

  7. Analysis of genetic diversity and estimation of inbreeding coefficient ...

    African Journals Online (AJOL)

    Analysis of genetic diversity and estimation of inbreeding coefficient within ... The present work is a contribution to the knowledge of population structure and to the ... diversity that may be helpful to horse breeders in designing and managing ...

  8. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    Free-living, heterotrophic protozoa have an important ecological role in most terrestrial ecosystems by their grazing of bacteria as one of the first links in food chains and webs. Furthermore, some of them serve as reservoirs for disease-causing bacteria and /or as occasional opportunistic...... pathogens themselves. Protozoa is a morphological group which occurs in many different eukaryotic phyla, and many apparently morphologically similar types are very different from each others genetically. This complicates the development of good primers for analysis of their diversity with modern DNA based...... methods. Compared to other microorganisms such as fungi, algae and bacteria, much less is known about protozoa. It has been an essential element of this thesis to to advance our knowledge of protozoa by developing new primers for DNA-based studies of protozoa impact on ecosystems or as indicators...

  9. Genetic diversity and molecular epidemiology of Anaplasma.

    Science.gov (United States)

    Battilani, Mara; De Arcangeli, Stefano; Balboni, Andrea; Dondi, Francesco

    2017-04-01

    Anaplasma are obligate intracellular bacteria of cells of haematopoietic origin and are aetiological agents of tick-borne diseases of both veterinary and medical interest common in both tropical and temperate regions. The recent disclosure of their zoonotic potential has greatly increased interest in the study of these bacteria, leading to the recent reorganisation of Rickettsia taxonomy and to the possible discovery of new species belonging to the genus Anaplasma. This review is particularly focused on the common and unique characteristics of Anaplasma marginale and Anaplasma phagocytophilum, with an emphasis on genetic diversity and evolution, and the main distinguishing features of the diseases caused by the different Anaplasma spp. are described as well. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Pyrosequencing and genetic diversity of microeukaryotes

    DEFF Research Database (Denmark)

    Harder, Christoffer Bugge

    Free-living, heterotrophic protozoa have an important ecological role in most terrestrial ecosystems by their grazing of bacteria as one of the first links in food chains and webs. Furthermore, some of them serve as reservoirs for disease-causing bacteria and /or as occasional opportunistic...... pathogens themselves. Protozoa is a morphological group which occurs in many different eukaryotic phyla, and many apparently morphologically similar types are very different from each others genetically. This complicates the development of good primers for analysis of their diversity with modern DNA based...... methods. Compared to other microorganisms such as fungi, algae and bacteria, much less is known about protozoa. It has been an essential element of this thesis to to advance our knowledge of protozoa by developing new primers for DNA-based studies of protozoa impact on ecosystems or as indicators...

  11. Positive interactions between herbivores and plant diversity shape forest regeneration.

    Science.gov (United States)

    Cook-Patton, Susan C; LaForgia, Marina; Parker, John D

    2014-05-22

    The effects of herbivores and diversity on plant communities have been studied separately but rarely in combination. We conducted two concurrent experiments over 3 years to examine how tree seedling diversity, density and herbivory affected forest regeneration. One experiment factorially manipulated plant diversity (one versus 15 species) and the presence/absence of deer (Odocoileus virginianus). We found that mixtures outperformed monocultures only in the presence of deer. Selective browsing on competitive dominants and associational protection from less palatable species appear responsible for this herbivore-driven diversity effect. The other experiment manipulated monospecific plant density and found little evidence for negative density dependence. Combined, these experiments suggest that the higher performance in mixture was owing to the acquisition of positive interspecific interactions rather than the loss of negative intraspecific interactions. Overall, we emphasize that realistic predictions about the consequences of changing biodiversity will require a deeper understanding of the interaction between plant diversity and higher trophic levels. If we had manipulated only plant diversity, we would have missed an important positive interaction across trophic levels: diverse seedling communities better resist herbivores, and herbivores help to maintain seedling diversity.

  12. Evaluation of genetic diversity in barley (Hordeum vulgare L.) from ...

    African Journals Online (AJOL)

    User

    2015-06-03

    Jun 3, 2015 ... traits, genotypes in cluster III deserve consideration for directly developing high yielding barely varieties. The result of ... Criteria for the estimation of genetic diversity can be ...... Plant Genetic Resources Institute, Rome, Italy.

  13. Assessment of genetic diversity in Isabgol (Plantago ovata Forsk ...

    African Journals Online (AJOL)

    sandeep kaswan

    using random amplified polymorphic DNA ... RAPD markers appeared more informative than ISSR in determining the genetic ... Key words: Plantago ovata, molecular marker, RAPD, ISSR, genetic diversity, medicinal plant. .... monomorphic.

  14. Inbreeding and genetic diversity in dogs: results from DNA analysis.

    Science.gov (United States)

    Wade, Claire M

    2011-08-01

    This review assesses evidence from DNA analysis to determine whether there is sufficient genetic diversity within breeds to ensure that populations are sustainable in the absence of cross breeding and to determine whether genetic diversity is declining. On average, dog breeds currently retain approximately 87% of the available domestic canine genetic diversity. Requirements that breeding stock must be 'clear' for all genetic disorders may firstly place undue genetic pressure on animals tested as being 'clear' of known genetic disorders, secondly may contribute to loss of diversity and thirdly may result in the dissemination of new recessive disorders for which no genetic tests are available. Global exchange of genetic material may hasten the loss of alleles and this practice should be discussed in relation to the current effective population size of a breed and its expected future popularity. Genomic data do not always support the results from pedigree analysis and possible reasons for this are discussed.

  15. Environmental correlates of plant diversity in Korean temperate forests

    Science.gov (United States)

    Černý, Tomáš; Doležal, Jiří; Janeček, Štěpán; Šrůtek, Miroslav; Valachovič, Milan; Petřík, Petr; Altman, Jan; Bartoš, Michael; Song, Jong-Suk

    2013-02-01

    Mountainous areas of the Korean Peninsula are among the biodiversity hotspots of the world's temperate forests. Understanding patterns in spatial distribution of their species richness requires explicit consideration of different environmental drivers and their effects on functionally differing components. In this study, we assess the impact of both geographical and soil variables on the fine-scale (400 m2) pattern of plant diversity using field data from six national parks, spanning a 1300 m altitudinal gradient. Species richness and the slopes of species-area curves were calculated separately for the tree, shrub and herb layer and used as response variables in regression tree analyses. A cluster analysis distinguished three dominant forest communities with specific patterns in the diversity-environment relationship. The most widespread middle-altitude oak forests had the highest tree richness but the lowest richness of herbaceous plants due to a dense bamboo understory. Total richness was positively associated with soil reaction and negatively associated with soluble phosphorus and solar radiation (site dryness). Tree richness was associated mainly with soil factors, although trees are frequently assumed to be controlled mainly by factors with large-scale impact. A U-shaped relationship was found between herbaceous plant richness and altitude, caused by a distribution pattern of dwarf bamboo in understory. No correlation between the degree of canopy openness and herb layer richness was detected. Slopes of the species-area curves indicated the various origins of forest communities. Variable diversity-environment responses in different layers and communities reinforce the necessity of context-dependent differentiation for the assessment of impacts of climate and land-use changes in these diverse but intensively exploited regions.

  16. Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest

    OpenAIRE

    Chaverri, Gloriana; Garin, Inazio; Alberdi, Antton; Jimenez, Lide; Castillo-Salazar, Cristian; Aihartza, Joxerra

    2016-01-01

    Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied, particularly for taxa that are difficult to sample such as bats. Aiming to estimate the amount of cryptic diversity among bats of a Neotropical montane cloud forest in Talamanca Range—south-east Central America—, we performed a ...

  17. 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.......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....

  18. [Research Progress on Genetic Diversity in Animal Parasitic Nematodes].

    Science.gov (United States)

    YIN, Fang-yuan; LI, Fa-cai; ZHAO, Jun-long; HU, Min

    2015-10-01

    The development of molecular genetic markers for parasitic nematodes has significant implications in fundamental and applied research in Veterinary Parasitology. Knowledge on genetic diversity of nematodes would not only provide a theoretical basis for understanding the spread of drug-resistance alleles, but also have implications in the development of nematode control strategies. This review discusses the applications of molecular genetic markers (RFLP, RAPD, PCR-SSCP, AFLP, SSR and mitochondrial DNA) in research on the genetic diversity of parasitic nematodes.

  19. Forest structure, diversity and soil properties in a dry tropical forest in Rajasthan, Western India

    Directory of Open Access Journals (Sweden)

    J. I. Nirmal Kumar

    2011-06-01

    Full Text Available Structure, species composition, and soil properties of a dry tropical forest in Rajasthan Western India, were examined by establishment of 25 plots. The forest was characterized by a relatively low canopy and a large number of small-diameter trees. Mean canopy height for this forest was 10 m and stands contained an average of 995 stems ha-1 (= 3.0 cm DBH; 52% of those stems were smaller than 10 cm DBH. The total basal area was 46.35 m2ha-1, of which Tectona grandis L. contributed 48%. The forest showed high species diversity of trees. 50 tree species (= 3.0 cm DBH from 29 families were identified in the 25 sampling plots. T. grandis (20.81% and Butea monosperma (9% were the dominant and subdominant species in terms of importance value. The mean tree species diversity indices for the plots were 1.08 for Shannon diversity index (H´, 0.71 for equitability index (J´ and 5.57 for species richness index (S´, all of which strongly declined with the increase of importance value of the dominant, T. grandis. Measures of soil nutrients indicated low fertility, extreme heterogeneity. Regression analysis showed that stem density and the dominant tree height were significantly correlated with soil pH. There was a significant positive relationship between species diversity index and soil available P, exchangeable K+, Ca2+ (all p values < 0.001 and a negative relationship with N, C, C:N and C:P ratio. The results suggest that soil properties are major factors influencing forest composition and structure within the dry tropical forest in Rajasthan.

  20. Genetic diversity in the Yangtze finless porpoise by RAPD analysis

    Institute of Scientific and Technical Information of China (English)

    He Shunping; Wang Ding; Wang Wei; Chen Daoquan; Zhao Qingzhong; Gong Weiming

    2005-01-01

    To estimate the genetic diversity in the Yangtze finless porpoise (Neophocaenaphocaenoides asiaeorientalis), the randomly amplified polymorphic DNA techniquewas applied to examine ten animals captured from the Yangtze River. Out of 20 arbitrary primers used in the experiment, seventeen produced clearly reproducible bged from 0.0986 to 0.5634. Compared with other cetacean populations, this genetic distance is quite low. Such a low genetic diversity suggests that this population may be suffering from reduced genetic variation, and be very fragile. More studiesare needed for understanding the basis for this apparent low genetic diversity and to help protect this endangered, unique population.

  1. Dominance and Diversity of Bird Community in Floodplain Forest Ecosystem

    Directory of Open Access Journals (Sweden)

    Karel Poprach

    2015-01-01

    Full Text Available The paper is aimed to assessment of diversity and structure of bird community in floodplain forest ecosystem. Authors present results of analyses data on bird communities obtained at two transects in the Litovelské Pomoraví Protected Landscape Area (Czech Republic in the period 1998–2012. Research of bird communities was carried out using the point-count method. The article deals with qualitative and quantitative representation of breeding bird species, including their relation to habitat type (closed floodplain forest, ecotone. Altogether 63 breeding species were recorded at the Vrapač transect and 67 at the Litovelské luhy transect, respectively. To be able to detect all recorded species, 11 out of 14 years of monitoring were needed at the Vrapač transect and all 8 years of monitoring at the Litovelské luhy transect, respectively. Authors show that the values in dominant bird species change significantly among the particular census dates within one season, mainly with respect to their activity and detectability. Results are discussed in the frame of sustainable forest management in floodplain forest ecosystems. The presented article can promote to discussion aimed to management strategy for floodplain forest ecosystems, which ranks among natural habitat types of Community interest protected under the Natura 2000 European network.

  2. Comparing the plant diversity between artificial forest and nature growth forest in a giant panda habitat.

    Science.gov (United States)

    Kang, Dongwei; Wang, Xiaorong; Li, Shuang; Li, Junqing

    2017-06-15

    Artificial restoration is an important way to restore forests, but little is known about its effect on the habitat restoration of the giant panda. In the present study, we investigated the characteristics of artificial forest in the Wanglang Nature Reserve to determine whether through succession it has formed a suitable habitat for the giant panda. We compared artificial forest characteristics with those of natural habitat used by the giant panda. We found that the dominant tree species in artificial forest differed from those in the natural habitat. The artificial forest had lower plant species richness and diversity in the tree and shrub layers than did the latter, and its community structure was characterized by smaller tree and bamboo sizes, and fewer and lower bamboo clumps, but more trees and larger shrub sizes. The typical community collocation of artificial forest was a "Picea asperata + no-bamboo" model, which differs starkly from the giant panda's natural habitat. After several years of restoration, the artificial forest has failed to become a suitable habitat for the giant panda. Therefore, a simple way of planting individual trees cannot restore giant panda habitat; instead, habitat restoration should be based on the habitat requirements of the giant panda.

  3. 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

  4. Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico.

    Science.gov (United States)

    Blair, Christopher; Jiménez Arcos, Victor H; Mendez de la Cruz, Fausto R; Murphy, Robert W

    2013-01-01

    Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.

  5. Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico.

    Directory of Open Access Journals (Sweden)

    Christopher Blair

    Full Text Available Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.

  6. [Soil microbial functional diversity of different altitude Pinus koraiensis forests].

    Science.gov (United States)

    Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

    2015-12-01

    In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

  7. Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm.

    Science.gov (United States)

    da Silva Carvalho, C; Ribeiro, M C; Côrtes, M C; Galetti, M; Collevatti, R G

    2015-09-01

    Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.

  8. Understanding crop genetic diversity under modern plant breeding.

    Science.gov (United States)

    Fu, Yong-Bi

    2015-11-01

    Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.

  9. The U.S. Forest Service National Seed Laboratory and Fraxinus ex situ genetic conservation

    Science.gov (United States)

    Robert P. Karrfalt

    2010-01-01

    The U.S. Forest Service's National Seed Laboratory (NSL) has as part of its mission the conservation of genetic resources for the Forest Service and Forest Service cooperators through long-term seed storage. The Forest Service recognizes ash as one of four priority species for genetic conservation. The NSL is in charge of the Forest Service ash preservation plan...

  10. Genetic Diversity of RAPD Mark for Natural Davidia involucrata Populations

    Institute of Scientific and Technical Information of China (English)

    Congwen Song; Manzhu Bao

    2006-01-01

    The genetic diversity and genetic variation within and among populations of five natural Davidia involucrata populations were studied from 13 primers based on random amplified polymorphic DNA (RAPD) analysis.The results show that natural D.involucrata population has a rich genetic diversity,and the differences among populations are significant.Twenty-six percent of genetic variation exists among D.involucrata populations,which is similar to that of the endangered tree species Liriodendron chinense and Cathaya argyrophylla in China,but different from more widely distributed tree species.The analysis of the impacts of sampling method on genetic diversity parameters shows that the number of sampled individuals has little effect on the effective number of alleles and genetic diversity,but has a marked effect on the genetic differentiation among populations and gene flows.This study divides the provenances of D.involucrata into two parts,namely,a southeast and a northwest provenance.

  11. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    Science.gov (United States)

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  12. Genetic diversity of human RNase 8

    Directory of Open Access Journals (Sweden)

    Chan Calvin C

    2012-01-01

    Full Text Available Abstract Background Ribonuclease 8 is a member of the RNase A family of secretory ribonucleases; orthologs of this gene have been found only in primate genomes. RNase 8 is a divergent paralog of RNase 7, which is lysine-enriched, highly conserved, has prominent antimicrobial activity, and is expressed in both normal and diseased skin; in contrast, the physiologic function of RNase 8 remains uncertain. Here, we examine the genetic diversity of human RNase 8, a subject of significant interest given the existence of functional pseudogenes (coding sequences that are otherwise intact but with mutations in elements crucial for ribonucleolytic activity in non-human primate genomes. Results RNase 8 expression was detected in adult human lung, spleen and testis tissue by quantitative reverse-transcription PCR. Only two single-nucleotide polymorphisms and four unique alleles were identified within the RNase 8 coding sequence; nucleotide sequence diversity (π = 0.00122 ± 0.00009 per site was unremarkable for a human nuclear gene. We isolated transcripts encoding RNase 8 via rapid amplification of cDNA ends (RACE and RT-PCR which included a distal potential translational start site followed by sequence encoding an additional 30 amino acids that are conserved in the genomes of several higher primates. The distal translational start site is functional and promotes RNase 8 synthesis in transfected COS-7 cells. Conclusions These results suggest that RNase 8 may diverge considerably from typical RNase A family ribonucleases and may likewise exhibit unique function. This finding prompts a reconsideration of what we have previously termed functional pseudogenes, as RNase 8 may be responding to constraints that promote significant functional divergence from the canonical structure and enzymatic activity characteristic of the RNase A family.

  13. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Directory of Open Access Journals (Sweden)

    Annika M E Noreen

    Full Text Available Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter, 193 saplings (>1 yr, and 1,822 seedlings (<1 yr of the canopy tree Koompassia malaccensis (Fabaceae. We tested hypotheses relevant to the genetic consequences of habitat loss: (1 that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2 K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854, high allelic richness (R = 16.7-19.5, low inbreeding co-efficients (FIS = 0.013-0.076, and a large proportion (30.1% of rare alleles (i.e. frequency <1%. However, spatial genetic structure (SGS analyses showed significant differences between the adults and the recruits. We detected significantly greater SGS intensity, as well as higher relatedness in the 0-10 m distance class, for seedlings and saplings compared to the adults. Demographic factors for this population (i.e. <200 adult trees are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961, calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  14. Endemic insular and coastal Tunisian date palm genetic diversity.

    Science.gov (United States)

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm.

  15. Beauveria bassiana: Quercetinase production and genetic diversity

    Science.gov (United States)

    Eula Maria de M. B., Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valéria de, Oliveira; Marília, Oliveira; Elda, Bueno; Silvana, Petrofeza

    2011-01-01

    Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase. PMID:24031599

  16. Beauveria bassiana: quercetinase production and genetic diversity

    Directory of Open Access Journals (Sweden)

    Eula Maria de M. B Costa

    2011-03-01

    Full Text Available Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min and isolate IP 11 (27.5 nmol/ml/min showed the best performances and IP 3a (9.5 nmol/mL/min presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase.

  17. Molecular genetic tools to infer the origin of forest plants and wood.

    Science.gov (United States)

    Finkeldey, Reiner; Leinemann, Ludger; Gailing, Oliver

    2010-02-01

    Most forest tree species exhibit high levels of genetic diversity that can be used to trace the origin of living plants or their products such as timber and processed wood. Recent progress to isolate DNA not only from living tissue but also from wood and wood products offers new opportunities to test the declared origin of material such as seedlings for plantation establishment or timber. However, since most forest tree populations are weakly differentiated, the identification of genetic markers to differentiate among spatially isolated populations is often difficult and time consuming. Two important fields of "forensic" applications are described: Molecular tools are applied to test the declared origin of forest reproductive material used for plantation establishment and of internationally traded timber and wood products. These applications are illustrated taking examples from Germany, where mechanisms have been developed to improve the control of the trade with forest seeds and seedlings, and from the trade with wood of the important Southeast Asian tree family Dipterocarpaceae. Prospects and limitations of the use of molecular genetic methods to conclude on the origin of forest plants, wood, and wood products are discussed.

  18. Strategy for the Conservation and Sustainable Use of Spanish Forest Genetic Resources

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, P.; Diaz-Fernandez, P. M.; Iglesias, S.; Prada, A.; Garcia del Barrio, J. M.; Alba, N.; Alia, R.

    2009-07-01

    In the last decade, forestry policies in Spain have undergone changes needed to comply with the European and world directives on forest conservation. The elaboration of strategic plans has to take into account the State organization (Central and Autonomous Regional Governments share the responsibilities), resulting in agreed documents, effective at a national level and fulfilling the peculiarities and aspirations of each region. The most recent development has been the elaboration of a Strategy for Conservation and Sustainable Use of Forest Genetic Resources, which can be seen as a consequence of, among other factors, the implementation of the Spanish Strategy for Conservation and Sustainable Use of Biodiversity along with Spains participation in the European Forest Genetic Resources Programme. This document arose from the lack of approaches to the conservation of population diversity of forest species in the current policies, and as a means to promote and coordinate activities on conservation and use of genetic resources. The Strategy has been arranged through a participative process involving the Forest Administration, Research Centres and Universities. The document includes a definition of priorities and proposals of activities, which are mainly focused on optimising the efficiency of existing tools and infrastructures and on increasing synergy among different initiatives. Implementation of the Strategy is expected to occur through the development of National Action Plans. Finally, coordination mechanisms must be enhanced in order to maintain the levels of cooperation achieved during the elaboration process. (Author) 18 refs.

  19. Diversity of Medicinal Plants among Different Forest-use Types of the Pakistani Himalaya.

    Science.gov (United States)

    Adnan, Muhammad; Hölscher, Dirk

    2012-12-01

    Diversity of Medicinal Plants among Different Forest-use Types of the Pakistani Himalaya Medicinal plants collected in Himalayan forests play a vital role in the livelihoods of regional rural societies and are also increasingly recognized at the international level. However, these forests are being heavily transformed by logging. Here we ask how forest transformation influences the diversity and composition of medicinal plants in northwestern Pakistan, where we studied old-growth forests, forests degraded by logging, and regrowth forests. First, an approximate map indicating these forest types was established and then 15 study plots per forest type were randomly selected. We found a total of 59 medicinal plant species consisting of herbs and ferns, most of which occurred in the old-growth forest. Species number was lowest in forest degraded by logging and intermediate in regrowth forest. The most valuable economic species, including six Himalayan endemics, occurred almost exclusively in old-growth forest. Species composition and abundance of forest degraded by logging differed markedly from that of old-growth forest, while regrowth forest was more similar to old-growth forest. The density of medicinal plants positively correlated with tree canopy cover in old-growth forest and negatively in degraded forest, which indicates that species adapted to open conditions dominate in logged forest. Thus, old-growth forests are important as refuge for vulnerable endemics. Forest degraded by logging has the lowest diversity of relatively common medicinal plants. Forest regrowth may foster the reappearance of certain medicinal species valuable to local livelihoods and as such promote acceptance of forest expansion and medicinal plants conservation in the region. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12231-012-9213-4) contains supplementary material, which is available to authorized users.

  20. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Science.gov (United States)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  1. High genetic diversity in a potentially vulnerable tropical tree species despite extreme habitat loss.

    Science.gov (United States)

    Noreen, Annika M E; Webb, Edward L

    2013-01-01

    Over the last 150 years, Singapore's primary forest has been reduced to less than 0.2% of its previous area, resulting in extinctions of native flora and fauna. Remaining species may be threatened by genetic erosion and inbreeding. We surveyed >95% of the remaining primary forest in Singapore and used eight highly polymorphic microsatellite loci to assess genetic diversity indices of 179 adults (>30 cm stem diameter), 193 saplings (>1 yr), and 1,822 seedlings (tree Koompassia malaccensis (Fabaceae). We tested hypotheses relevant to the genetic consequences of habitat loss: (1) that the K. malaccensis population in Singapore experienced a genetic bottleneck and a reduction in effective population size, and (2) K. malaccensis recruits would exhibit genetic erosion and inbreeding compared to adults. Contrary to expectations, we detected neither a population bottleneck nor a reduction in effective population size, and high genetic diversity in all age classes. Genetic diversity indices among age classes were not significantly different: we detected overall high expected heterozygosity (He = 0.843-0.854), high allelic richness (R = 16.7-19.5), low inbreeding co-efficients (FIS = 0.013-0.076), and a large proportion (30.1%) of rare alleles (i.e. frequency trees) are a cause for concern, as rare alleles could be lost due to stochastic factors. The high outcrossing rate (tm = 0.961), calculated from seedlings, may be instrumental in maintaining genetic diversity and suggests that pollination by highly mobile bee species in the genus Apis may provide resilience to acute habitat loss.

  2. Tree diversity and economic importance of forest trees of Kashmir (Jammu and Kashmir

    Directory of Open Access Journals (Sweden)

    Sajad Ali Lone

    2013-12-01

    Full Text Available Aim The paper throws light on diversity of trees of forests of Kashmir of Jammu And Kashmir State. Methodology: Present study is based on the extensive and intensive field surveys made during 2007-2008. Various forest areas were visited for the identification of tree species and their economic importance. Various forest areas were visited for the identification of tree species and their economic importance. The areas including Drang Tangmerg, Gulmarg, Dachigam, Lolab and Karanah valley. Information on the utilization of trees for curing common ailments was obtained from people of the above forest areas. Conversation regarding the economic importance of plants was especially done with the elderly men, hakims and tribals. Repeated queries were made to get the data verified and confirmed. The plant specimens were dried using the standard herbarium techniques. The specimens were identified using Hooker method. Wherever necessary, comparisons were made with herbarium specimens in the herbarium of Forest Research Institute, Dehradun. Survey Results: Botanical names, English/common/local/Vernacular names, family, fruiting and flowering period, distribution and uses (wherever known of 53 species belonging to 33 genera and 21 families are provided. Conclusion: Present study has revealed the occurrence of 53 species belonging to 33 genera under 21 families. The most dominant family as per the number of genera is Pinaceae family followed by Betulaceae. And the most dominant genera is Prunus which is having 6 species. The study reveals that there are 10 gymnosperms and 43 angiosperms in the forests of Kashmir. The present work gives a detailed account of economic importance of forest trees of Kashmir. The work shows the relevance of plants to the problems of health care, food, agriculture improvements, conservation of genetic resources and to economic welfare of the tribal is emphasized. The work should rightly be applied to the natural and direct

  3. Genetic Diversity of Parkia biglobosa from Different Agroecological Zones of Nigeria Using RAPD Markers

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    Oluwafemi Amusa

    2014-01-01

    Full Text Available Parkia biglobosa (Jacq. is an important leguminous tree crop in the African Savannahs useful to the natives where it is found, for domestic use. Previous diversity studies on this tree crop had been majorly on morphological and biochemical analysis. In order to capture the maximum diversity not obtained by previous research, the study aimed at evaluating the genetic diversity of accessions of this crop in the different agroecological zones in Nigeria using RAPD markers. A total of 81 scorable bands with an average of 8.1 bands per primer were amplified among the accessions studied. Intrazonal genetic diversity analysis showed a percentage polymorphism with a range of 11.11% to 65.43% among the agroecological zones studied. Although, gene diversity was highest within Humid forest agroecological zone, a low genetic distance and high genetic similarity between the agroecological zones were observed. Cluster analysis indicated six main groups of which four groups had single accessions while the two groups clustered the remaining accessions, indicating a narrowed genetic base from the 23 accessions studied.

  4. Spatial pattern of tree diversity and evenness across forest types in Majella National Park, Italy

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    Mohammad Redowan

    2015-09-01

    Full Text Available Background Estimation of tree diversity at broader scale is important for conservation planning. Tree diversity should be measured and understood in terms of diversity and evenness, two integral components to describe the structure of a biological community. Variation of the tree diversity and evenness with elevation, topographic relief, aspect, terrain shape, slope, soil nutrient, solar radiation etc. are well documented. Methods Present study explores the variation of tree diversity (measured as Shannon diversity and evenness indices of Majella National Park, Italy with five available forest types namely evergreen oak woods, deciduous oak woods, black/aleppo pine stands, hop-hornbeam forest and beech forest, using satellite, environmental and field data. Results Hop-hornbeam forest was found to be most diverse and even while evergreen Oak woods was the lowest diverse and even. Diversity and evenness of forest types were concurrent to each other i.e. forest type which was more diverse was also more even. As a broad pattern, majority portion of the study area belonged to medium diversity and high evenness class. Conclusions Satellite images and other GIS data proved useful tools in monitoring variation of tree diversity and evenness across various forest types. Present study findings may have implications in prioritizing conservation zones of high tree diversity at Majella.

  5. Extreme genetic diversity in asexual grass thrips populations.

    Science.gov (United States)

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.

  6. Tree species diversity effects on soil microbial biomass, diversity and activity across European forest types

    OpenAIRE

    Carnol, Monique; Baeten, Lander; Bosman, Bernard; De Wandeler, Hans; Muys, Bart

    2014-01-01

    Increasing tree species diversity in forests might contribute to ecosystem-service maintenance, as well as to the reconciliation of regulating, provisioning and supporting services within the frame of multifunctional and sustainable forestry. Individual tree species influence biogeochemical cycling through element deposition (throughfall, litterfall), and through microbial activities in the soil. Yet, the influence of mixing tree species on these ecosystem processes is unclear, in particular ...

  7. Does genetic diversity hinder parasite evolution in social insect colonies?

    DEFF Research Database (Denmark)

    Hughes, William Owen Hamar; Boomsma, Jacobus Jan

    2006-01-01

    of host genetic diversity on parasite evolution by carrying out serial passages of a virulent fungal pathogen through leaf-cutting ant workers of known genotypes. Parasite virulence increased over the nine-generation span of the experiment while spore production decreased. The effect of host relatedness......Polyandry is often difficult to explain because benefits of the behaviour have proved elusive. In social insects, polyandry increases the genetic diversity of workers within a colony and this has been suggested to improve the resistance of the colony to disease. Here we examine the possible impact...... upon virulence appeared limited. However, parasites cycled through more genetically diverse hosts were more likely to go extinct during the experiment and parasites cycled through more genetically similar hosts had greater spore production. These results indicate that host genetic diversity may indeed...

  8. Biological diversity of created forested wetlands in comparison to reference forested wetlands in the Bay watershed

    Science.gov (United States)

    Perry, M.C.; Osenton, P.C.; Stoll, C.S.; Therres, Glenn D.

    2001-01-01

    Amphibians, reptiles, birds, and mammals were surveyed at six created forested wetlands in central Maryland and at six adjacent reference forested wetlands during 1993-1996 to determine comparative biological diversity of these habitats. Amphibians and reptiles were caught in pitfall and funnel traps associated with 15.4m (50 ft) drift fences. Birds were surveyed with a complete count while walking through each area. Mammals were surveyed by capture in live traps. More species and total individuals of amphibians were caught on the reference wetlands than on the created wetlands. The red-backed salamander (Plethodon cinereus), the four-toed salamander (Hemidactylium scutatum), the eastern spadefoot (Scaphiopus holbrooki), and the wood frog (Rana sylvatica) were captured on the reference wetlands, but not on the created sites. The wood frog was captured at all reference sites and may represent the best amphibian species to characterize a forested wetland. Reptiles were not caught in sufficient numbers to warrant comparisons. Ninety-two bird species were recorded on created sites and 55 bird species on the reference sites. Bird species on the created sites represented those typically found in nonforested habitats. Mammal species were similar on both sites, but overall the reference sites had three times the number caught on created sites. The meadow vole (Microtus pennsylvanicus) was the dominant species captured on created sites, and the white-footed mouse (Peromyscus leucopus) was the dominant species on reference sites, with little habitat overlap for these two species. Although species richness and total number of animals were high for created forested wetlands, these survey results show major differences from species expected for a forested wetland. The created forested wetlands appear to provide good habitat for wildlife, but are probably not providing the full functions and values of the forested wetlands that they were constructed to replace.

  9. Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert.) O. Kuntze relict populations

    Science.gov (United States)

    2009-01-01

    Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five “genetic clusters” (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three “genetic clusters”. These results are in agreement with the pattern of geographic distribution of the studied populations. PMID:21637518

  10. Genetic diversity increases insect herbivory on oak saplings.

    Directory of Open Access Journals (Sweden)

    Bastien Castagneyrol

    Full Text Available A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect. Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores.

  11. Plant diversity in hedgerows amidst Atlantic Forest fragments

    Directory of Open Access Journals (Sweden)

    Carolina C. C. Oliveira

    2015-06-01

    Full Text Available Hedgerows are linear structures found in agricultural landscapes that may facilitate dispersal of plants and animals and also serve as habitat. The aim of this study was to investigate the relationships among diversity and ecological traits of woody plants, hedgerow characteristics (size, age, and origin, and the structure of the surrounding Atlantic Forest landscape. Field data were collected from 14 hedgerows, and landscape metrics from 1000-m buffers surrounding hedgerows were recorded from a thematic map. In all sampled hedgerows, arboreal species were predominantly zoochoric and early-succession species, and hedgerow width was an important factor explaining the richness and abundance of this group of species. Connection with forest vegetation did not explain richness and abundance of animal-dispersed species, but richness of non-zoochoric species increased in more connected hedgerows. These results suggest that hedgerows are probably colonized by species arriving from nearby early-succession sites, forest fragment edges, and isolated trees in the matrix. Nonetheless, hedgerows provide resources for frugivorous animals and influence landscape connectivity, highlighting the importance of these elements in the conservation of biodiversity in fragmented and rural landscapes.

  12. Stand structural diversity rather than species diversity enhances aboveground carbon storage in secondary subtropical forests in Eastern China

    Science.gov (United States)

    Ali, Arshad; Yan, En-Rong; Chen, Han Y. H.; Chang, Scott X.; Zhao, Yan-Tao; Yang, Xiao-Dong; Xu, Ming-Shan

    2016-08-01

    Stand structural diversity, typically characterized by variances in tree diameter at breast height (DBH) and total height, plays a critical role in influencing aboveground carbon (C) storage. However, few studies have considered the multivariate relationships of aboveground C storage with stand age, stand structural diversity, and species diversity in natural forests. In this study, aboveground C storage, stand age, tree species, DBH and height diversity indices, were determined across 80 subtropical forest plots in Eastern China. We employed structural equation modelling (SEM) to test for the direct and indirect effects of stand structural diversity, species diversity, and stand age on aboveground C storage. The three final SEMs with different directions for the path between species diversity and stand structural diversity had a similar goodness of fit to the data. They accounted for 82 % of the variation in aboveground C storage, 55-59 % of the variation in stand structural diversity, and 0.1 to 9 % of the variation in species diversity. Stand age demonstrated strong positive total effects, including a positive direct effect (β = 0.41), and a positive indirect effect via stand structural diversity (β = 0.41) on aboveground C storage. Stand structural diversity had a positive direct effect on aboveground C storage (β = 0.56), whereas there was little total effect of species diversity as it had a negative direct association with, but had a positive indirect effect, via stand structural diversity, on aboveground C storage. The negligible total effect of species diversity on aboveground C storage in the forests under study may have been attributable to competitive exclusion with high aboveground biomass, or a historical logging preference for productive species. Our analyses suggested that stand structural diversity was a major determinant for variations in aboveground C storage in the secondary subtropical forests in Eastern China. Hence, maintaining tree DBH and

  13. Population Genetic Diversity in the Australian 'Seascape': A Bioregion Approach.

    Directory of Open Access Journals (Sweden)

    Lisa C Pope

    Full Text Available Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA bioregions, latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4. Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a 'hump' in diversity across the range studied (-9.4 to -43.7°S. Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales.

  14. Genetic diversity in soybean genotypes with resistance to Heterodera glycines

    Directory of Open Access Journals (Sweden)

    Ana Paula Oliveira Nogueira

    2011-01-01

    Full Text Available The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heteroderaglycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics andresistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by themethod of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimatedcoefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variabilitywas maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode

  15. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  16. The impact of forest roads on understory plant diversity in temperate hornbeam-beech forests of Northern Iran.

    Science.gov (United States)

    Deljouei, Azade; Abdi, Ehsan; Marcantonio, Matteo; Majnounian, Baris; Amici, Valerio; Sohrabi, Hormoz

    2017-08-01

    Forest roads alter the biotic and abiotic components of ecosystems, modifying temperature, humidity, wind speed, and light availability that, in turn, cause changes in plant community composition and diversity. We aim at investigating and comparing the diversity of herbaceous species along main and secondary forest roads in a temperate-managed hornbeam-beech forest, north of Iran. Sixteen transects along main and secondary forest roads were established (eight transects along main roads and eight along secondary roads). To eliminate the effect of forest type, all transects were located in Carpinetum-Fagetum forests, the dominant forest type in the study area. The total length of each transect was 200 m (100 m toward up slope and 100 m toward down slope), and plots were established along it at different distances from road edge. The diversity of herbaceous plant species was calculated in each plot using Shannon-Wiener index, species richness, and Pielou's index. The results showed that diversity index decreased when distance from road edge increases. This decreasing trend continued up to 60 m from forest road margin, and after this threshold, the index slightly increased. Depending on the type of road (main or secondary) as well as cut or fill slopes, the area showing a statistical different plant composition and diversity measured through Shannon-Wiener, species richness, and Pielou's index is up to 10 m. The length depth of the road edge effect found in main and secondary forest roads was small, but it could have cumulative effects on forest microclimate and forest-associated biota at the island scale. Forest managers should account for the effect of road buildings on plant communities.

  17. Genetic diversity in introduced populations with an Allee effect.

    Science.gov (United States)

    Wittmann, Meike J; Gabriel, Wilfried; Metzler, Dirk

    2014-09-01

    A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations.

  18. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding.

    Science.gov (United States)

    Holliday, Jason A; Aitken, Sally N; Cooke, Janice E K; Fady, Bruno; González-Martínez, Santiago C; Heuertz, Myriam; Jaramillo-Correa, Juan-Pablo; Lexer, Christian; Staton, Margaret; Whetten, Ross W; Plomion, Christophe

    2017-02-01

    Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.

  19. Assessment of genetic diversity in Triticum spp. and Aegilops spp ...

    African Journals Online (AJOL)

    SERVER

    2008-03-04

    Mar 4, 2008 ... 83111, Iran. 2Ilam Agricultural Research Center, Ilam-69317 73834, Iran. ... important food crops such as wheat and its wild relatives. These species ..... diversity trends during domestication and breeding. Theor. Appl. Genet.

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

    African Journals Online (AJOL)

    Genetic diversity of Ghanaian local chicken populations based on ... raised across distinct agro-ecological zones and constitute unique populations with variable ... (GHFO) in the southwest and the Coastal Savannah (GHCS) along the coast in ...

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

    African Journals Online (AJOL)

    STORAGESEVER

    2008-07-18

    Jul 18, 2008 ... A. senegal is widely distributed because it tolerates .... Locations of study areas for genetic diversity study of A. senegal in Kenya situated in four districts of ..... Molecular Biology and Biotechnology Center, University of Alberta,.

  2. Analysis of Genetic diversity and reltionships in local Tunisian barley ...

    African Journals Online (AJOL)

    Yomi

    Key words: Barley, RAPD markers, SSR markers, genetic diversity. INTRODUCTION. Barley ... surveyed by each kind of marker, their distribution ..... that belong to the Center. ..... tagged-site facilitated PCR for barley genome mapping. Theor.

  3. 1 Hierarchical Approaches to the Analysis of Genetic Diversity in ...

    African Journals Online (AJOL)

    2015-04-14

    Apr 14, 2015 ... Keywords: Genetic diversity, Hierarchical approach, Plant, Clustering,. Descriptive ... utilization) or by clustering (based on a phonetic analysis of individual ...... Improvement of Food Crop Preservatives for the next Millennium.

  4. analysis of genetic diversity in linseed using aflp markers

    African Journals Online (AJOL)

    ADMIN

    environments, enhanced resistance to pathogens, pests and other ... parental genotypes are often selected on the basis of phenotypic ..... M. Sc. Thesis, ... Genotype-environment interactions and ... genetic diversity assessment among wheat.

  5. Study on genetic diversity in Pakistani wheat varieties using simple ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-01

    Sep 1, 2009 ... genetic diversity of 10 varieties of wheat (T. aestivum) were analyzed using 14 simple sequence repeat. (SSR) primer sets ... wheat every year. To increase .... All PCR reactions were carried out in 25 µl reaction containing 50 -.

  6. Assessing the genetic diversity of cultivars and wild soybeans using ...

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... In this study, we demonstrated the differences of genetic diversity level among 40 soybean accessions of ... It has many advantages, including .... several other provinces abroad and of unknown origin; as control and these ...

  7. Assessment of the genetic diversity of geographically unrelated ...

    African Journals Online (AJOL)

    JOHN

    2005-05-05

    May 5, 2005 ... Key words: Molecular markers, distribution, cyanobacteria, genetic diversity. ..... Degree of polymorphism and average polymorphism information content (PIC) and marker index (MI) for the ..... monomorphic bands (Table 2).

  8. The relationship between species diversity and genetic structure in the rare Picea chihuahuana tree species community, Mexico.

    Science.gov (United States)

    Simental-Rodríguez, Sergio Leonel; Quiñones-Pérez, Carmen Zulema; Moya, Daniel; Hernández-Tecles, Enrique; López-Sánchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as "Endangered" on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between

  9. Influence of persistent monodominance on functional diversity and functional community assembly in African tropical forests.

    Science.gov (United States)

    Kearsley, Elizabeth; Verbeeck, Hans; Hufkens, Koen; Beeckman, Hans; Steppe, Kathy; Boeckx, Pascal; Huygens, Dries

    2015-04-01

    Lowland tropical rainforest are taxonomically diverse and complex systems, although not all tropical communities are equally diverse. Naturally occuring monodominant patches of Gilbertiodendron dewevrei are commonly found across Central Africa alongside higher diversity forests. Nevertheless, a low taxonomical diversity does not necessarily indicate an equivalently low functional diverse system. We investigate the functional diversity and functional community assembly of mixed and monodominant tropical forests in a central region of the Congo Basin in D. R. Congo using 15 leaf and wood traits covering 95% of all species within each community. This unique dataset allows us to investigate differences in functional diversity and ecosystem functioning between mixed and monodominant forest types. Functional richness, functional divergence and functional evenness are three functional diversity measures providing different aspects of functional diversity. The largest difference between the two forest types was found for functional richness, with a lower functional richness in the monodominant forest indicating a higher amount of niche space filled in the mixed forest. The mixed forest also had a higher species richness and Simpson diversity index, indicating that the higher species richness increases the functional niche space. Subsequently, we identified whole community trait shifts within the monodominant forest compared to the mixed forest. The dominance of Gilbertiodendron dewevrei, for which a distinct niche is found for most traits, presented a significant influence on the entire (trait) community expressing fundamental differences in ecosystem functioning. More detailed investigation of species unique within the monodominant forest and species occurring in both forest types provide more insight into the influence of Gilbertiodendron dewevrei. Both the unique and the shared species showed significant shifts in leaf nutrients, specific leaf area and water use

  10. Ectomycorrhizal fungal diversity, tree diversity and root nutrient relations in a mixed Central European forest.

    Science.gov (United States)

    Lang, Christa; Polle, Andrea

    2011-05-01

    Knowledge is limited about whether root nutrient concentrations are affected by mixtures of tree species and interspecific root competition. The goal of this field study was to investigate root nutrient element concentrations in relation to root and ectomycorrhizal (EM) diversity in six different mixtures of beech (Fagus sylvatica), ash (Fraxinus excelsior) and lime (Tilia sp.) in an old-growth, undisturbed forest ecosystem. Root biomass and nutrient concentrations per tree taxon as well as the abundance and identity of all EM fungi were determined in soil cores of a volume of 1 L (r=40 mm, depth=200 mm). Stand-level nutrient concentrations in overall root biomass and H' (Shannon-Wiener diversity) were obtained by pooling the data per stand. At stand level, Shannon H' for roots and aboveground tree species abundance were correlated. H' for roots and EM fungi were not correlated because of the contribution of ash roots that form only arbuscular mycorrhizal but no EM associations. Nutrient element concentrations in roots showed taxon-related differences and increased in the following order: beech ≤ lime tree diversity because of two effects: increasing contribution of ash roots to the mixture and increasing Ca accumulation in beech roots with increasing root diversity. On a small scale, increasing root diversity, but not EM diversity, was correlated with decreasing P concentrations in beech roots pointing to interspecific tree competition. Nitrogen (N) concentrations of beech roots were unaltered in relation to root and EM diversity. Opposing behavior was observed for lime and ash: the N concentrations in lime roots increased, whereas those in ash roots decreased with increasing EM diversity in a given soil volume. This suggests that EM diversity facilitates N acquisition of lime roots at the expense of non-EM ash.

  11. Plants Species Diversity in Hyrcanian Hardwood Forests, Northern Iran (Case Study: Mazandaran Province

    Directory of Open Access Journals (Sweden)

    Kambiz Abrari Vajari

    2013-12-01

    Full Text Available In order to better understand and manage forest ecosystems, it is important to study the relationship between environmental factors and plants in these ecosystems. We investigated plant species diversity of three hardwood forest stands in the Hyrcanian forests, Sari, northern Iran. Our aim was to determine the effect of forest stand type on the diversity of plant species. One plot 150 × 150 m established at the center of each forest stand and in each plot, nine subplots 50 × 50 m were selected. Diversity values (Richness, diversity and evenness indices were measured in five sample areas 0.01 ha per 50 × 50 m quadrates by estimating cover percentage of each species. The results showed that Geophytes (43.33% had the highest life form spectrum among species. JACCARD'S similarity index revealed that the highest values exist between Parrotia-Carpinus and Carpinus stands. All herb layer species diversity indices varied significantly among different forest stands. Cover percentage significantly positively correlated with diversity indices in Parrotia-Carpinus stand. Diversity and richness indices of herb-layers plants were significantly negatively correlated with cover percentage in Fagus stand. Correlation analysis between all diversity measures and cover percentage in Carpinus stand wasn't significant. The result of the present study revealed that species diversity in temperate broad-leaved deciduous forest was significantly influenced by forest stand type

  12. GENETIC DIVERSITY AND ECO-GEOGRAPHICAL DISTRIBUTION ...

    African Journals Online (AJOL)

    ACSS

    3Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia ... Allelic frequency based inter-species genetic distance analysis, showed wider .... taxonomy, evolution and origin of the species ...... Age International (P) Limited, New Delhi, India ... Integrated analysis environment for genetic.

  13. Contrasting taxonomic and phylogenetic diversity responses to forest modifications: comparisons of taxa and successive plant life stages in South African scarp forest.

    Science.gov (United States)

    Grass, Ingo; Brandl, Roland; Botzat, Alexandra; Neuschulz, Eike Lena; Farwig, Nina

    2015-01-01

    The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different

  14. Contrasting taxonomic and phylogenetic diversity responses to forest modifications: comparisons of taxa and successive plant life stages in South African scarp forest.

    Directory of Open Access Journals (Sweden)

    Ingo Grass

    Full Text Available The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic or to local (α-diversity and regional (β-diversity spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The

  15. Tree assemblages and diversity patterns in Tropical Juri Forest, Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Swapan Kumar Sarker; Muhammad Nur-Un-Nabi; Md. Mohasinul Haque; Mahmuda Sharmin; Sanjay Saha Sonet; Sourav Das; Niamjit Das

    2015-01-01

    Juri is a biodiversity-rich primary forest in Bangladesh, which remains ecologically unexplored. We identified tree species and examined the richness, alpha (α) diversity and floristic similarity patterns within the identi-fied communities. Vegetation and environmental data were sampled in 120 (0.04 ha) study plots. Tree communities were delimited by two-way indicator species analysis (TWINSPAN). In total, 78 tree species of 35 families and 58 genera were identified. TWINSPAN identified six tree communities: A—Tricalysia singularis; B—Kydia calyci-na-Castanopsis tribuloides;C—Polyalthia simiarum-Dua-banga grandiflora; D—Ficus roxburghii; E—Artocarpus lacucha;F—Artocarpus lacucha. Mean richness, Shannon and Gini-Simpson indices were highest for the Polyalthia simiarum-Duabanga grandiflora community, while Ficus roxburghii showed lowest diversity. Significant differences (p=0.05) in three diversity indices were recorded between Polyalthia simiarum-Duabanga grandiflora and Ficus roxburghii. Tree compositional similarity was greatest between Kydia calycina-Castanopsis tribuloides and Polyalthia simiarum-Duabanga grandiflora (0.712).

  16. Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters.

    Science.gov (United States)

    Souto, Cintia P; Mathiasen, Paula; Acosta, María Cristina; Quiroga, María Paula; Vidal-Russell, Romina; Echeverría, Cristian; Premoli, Andrea C

    2015-01-01

    Conservation planning requires setting priorities at the same spatial scale at which decision-making processes are undertaken considering all levels of biodiversity, but current methods for identifying biodiversity hotspots ignore its genetic component. We developed a fine-scale approach based on the definition of genetic hotspots, which have high genetic diversity and unique variants that represent their evolutionary potential and evolutionary novelties. Our hypothesis is that wide-ranging taxa with similar ecological tolerances, yet of phylogenetically independent lineages, have been and currently are shaped by ecological and evolutionary forces that result in geographically concordant genetic patterns. We mapped previously published genetic diversity and unique variants of biparentally inherited markers and chloroplast sequences for 9 species from 188 and 275 populations, respectively, of the 4 woody dominant families of the austral temperate forest, an area considered a biodiversity hotspot. Spatial distribution patterns of genetic polymorphisms differed among taxa according to their ecological tolerances. Eight genetic hotspots were detected and we recommend conservation actions for some in the southern Coastal Range in Chile. Existing spatially explicit genetic data from multiple populations and species can help to identify biodiversity hotspots and guide conservation actions to establish science-based protected areas that will preserve the evolutionary potential of key habitats and species.

  17. A call for tiger management using "reserves" of genetic diversity.

    Science.gov (United States)

    Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A

    2014-01-01

    Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.

  18. Investigating Genetic Diversity of Foeniculum Vulgare Mill using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Omid Jadidi

    2016-06-01

    Full Text Available Medicinal plants are considered valuable genetic resources in Iran. One of these medicinal as well as spice plants is Foeniculum Vulgare Mill from Umbellifetae family used in different industries such as food, medicine, and cosmetics. It seems that due to different climate conditions in Iran this plant represents a high and valuable genetic diversity; therefore, management of genetic resources protection and obtaining information about genetic diversity will help awareness of evolution processes as well as genetic erosion of this valuable plant. Genetic diversity in local masses of Foeniculum Vulgare Mill can be investigated using molecule markers such as AFLP, RAPD, ISSR, SRAP, RFLP, and so on. In investigation of over 30 ecotype of local Foeniculum Vulgare Mill, different markers have shown that mean polymorphic content (PIC is about 36% and mean genetic diversity is estimated about 40% in different samples. Data obtained from molecule software analyses help to categorize Foeniculum Vulgare Mill genotype in different groups based on climate and geographical conditions. Principle components analysis (PCOA has also confirmed the results of cluster analysis. Dendrogram obtained by cluster analysis based on similarity coefficient of simple matching (SM and UPGMA algorithm can also categorize population of Foeniculum Vulgare Mill in different groups. Results of molecular variance analysis (AMOVA have shown that most genetic variance between geographical groups can be seen in populations. In general, according to investigations, there is a significant genetic diversity regarding agronomic and molecular traits of Foeniculum Vulgare Mill masses in Iran and knowing this genetic diversity will help in breeding programs, complementary studies, categorization, and so on.

  19. Genetic diversity of seagrass seeds influences seedling morphology and biomass.

    Science.gov (United States)

    Randall Hughes, A; Hanley, Torrance C; Schenck, Forest R; Hays, Cynthia G

    2016-12-01

    Genetic diversity can influence ecological processes throughout ontogeny, yet whether diversity at early life history stages is important in long-lived taxa with overlapping generations is unclear. Seagrass systems provide some of the best evidence for the ecological effects of genetic diversity among adult shoots, but we do not know if the genetic diversity of seeds and seedlings also influences seagrass ecology. We tested the effects of seagrass (Zostera marina) seed diversity and relatedness on germination success, seedling morphology, and seedling production by comparing experimental assemblages of seeds collected from single reproductive shoots ("monocultures") to assemblages of seeds collected from multiple reproductive shoots ("polycultures"). There was no difference in seedling emergence, yet seedlings from polycultures had larger shoots above and below ground than seedlings from monocultures at the end of the 1-yr experiment. Genetic relatedness of the seedlings predicted some aspects of shoot morphology, with more leaves and longer roots and shoots at intermediate levels of relatedness, regardless of seed diversity. Our results suggest that studies of only adult stages may underestimate the importance of genetic diversity if the benefits at early life history stages continue to accrue throughout the life cycle. © 2016 by the Ecological Society of America.

  20. GENETIC DIVERSITY OF WHEAT CULTIVARS ESTIMATED BY SSR MARKERS

    Directory of Open Access Journals (Sweden)

    K. Dvojković

    2008-09-01

    Full Text Available Presence and utilization of the genetic variability in the breeding programmes is prerequisite for their successfulness. Important factor for crop improvement is knowledge about the genetic diversity which providing a basis for the precise selection of parental combinations. Since beginning of 20th century, generation of wheat breeders and scientists in Croatia developed numerous advanced and successful wheat cultivars. Previous researches aimed to genetic diversity evaluation in Croatia were conducted by means of morphological traits, pedigree data (coefficients of parentage, proteins (glutenins and gliadins and RAPD DNA markers. DNA markers detect directly variation of DNA sequence for particular loci and they are not under influence of environment, epistatic and pleiotropic effects. Microsatellite markers (Simple Sequence Repeats; SSRs, as highly polymorphic, informative and codominant DNA marker system, have been extensively used for genetic diversity studies on wheat world wide. A set of 98 wheat cultivars released in Croatia during the period 1905-2007, and 24 foreign cultivar (included because of their ancestral significance or as standards, were screened by 45 microsatellite markers, covering all three wheat genomes. The objectives of this study were to evaluate the microsatellites-based genetic diversity with emphasize on cultivars created at the Agricultural Institute Osijek, as well as to investigate SSR application for selection of genetically the most distant parental pairs. Preliminary data obtained by means of SSR markers showed a satisfactory level of genetic diversity and usefulness of microsatellites for parental selection.

  1. Diversity of filamentous fungi in organic layers of two forests in Zijin Mountain

    Institute of Scientific and Technical Information of China (English)

    SONGFu-qiang; TIANXing-Jun; LIZhong-Qi; YANGChang-Lin; CHENBin; HAOJie-jie; ZHUJing

    2004-01-01

    A study was conducted to evaluate the cultivable filamentous fungal diversity in organic layers (L, F, and H layers) and A1 layer of two main forest types, Pinus massoniana and Liguidambar formasana mixed forest and Quercus variabilis forest, in Zijin Mountain(32°5' N, 118°48'E), Nanjing, China. A total of 67 taxa comprising 56 Deuteromycetes, 3 Zygomycetes, 5 Ascomycetes and 3 unidentified fungi were recognized from samples from the forest floor of the two forest types. The most abundant group was Deuteromycetes. The dominant genera in both forests were Alternaria sp., Aspergillus sp., Cladosporium sp., Mucor sp., Penicillium sp., Rhizopus sp., Gliocladium sp. and Trichoderma spp. The fungal diversity was higher in the mixed forest than that in Q. variabilis forest. For both forest types, the maximum fungal diversity was found in layer F and there existed significantly different in fungal diversity between layer F and layer L In the mixed forest, richness of fungi isolated from needle litter (P.massoniana) was lower than that from leaf litter (L. formasana). The richness of fungi from needle litter increased with the increase of forest floor depth, but for leaf litter, the fungal diversity decreased with the depth of forest floor. The co-species of fungi from the two forest types, as well as from two kinds of litters in mixed forest, increased with the depth of the forest floor. The succession of fungi along with the process of decomposition was discussed here. The results also showed that litter quality was a cdtical factor affecting fungal diversity.

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

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... variation and, hence, restricting the amount of adapted genetic diversity ... the phenotypic diversity of common bean in Uganda. The selection ... The place of collection/origin was also consi- dered in ..... Bean Research and Development Programs at NaCRRI and CIAT .... Evolution 92:1101-1104. Kami JA ...

  3. The characterization of goat genetic diversity : Towards a genomic approach

    NARCIS (Netherlands)

    Ajmone-Marsan, P.; Colli, L.; Han, J. L.; Achilli, A.; Lancioni, H.; Joost, S.; Crepaldi, P.; Pilla, F.; Stella, A.; Taberlet, P.; Boettcher, P.; Negrini, R.; Lenstra, J. A.

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers fo

  4. Accumulation of genetic diversity in the US Potato Genebank

    Science.gov (United States)

    Efficient management of ex-situ collections includes understanding how conservation technologies impact the genetic diversity and integrity of these collections. For over 60 years, research at the US Potato Genebank has produced helpful scientific insights on diverse aspects of potato conservation. ...

  5. The characterization of goat genetic diversity : Towards a genomic approach

    NARCIS (Netherlands)

    Ajmone-Marsan, P.; Colli, L.; Han, J. L.; Achilli, A.; Lancioni, H.; Joost, S.; Crepaldi, P.; Pilla, F.; Stella, A.; Taberlet, P.; Boettcher, P.; Negrini, R.; Lenstra, J. A.|info:eu-repo/dai/nl/067852335

    2014-01-01

    The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers

  6. Composition, structure and diversity characterization of dry tropical forest of Chhattisgarh using satellite data

    Institute of Scientific and Technical Information of China (English)

    Tarun Thakur; S.L. Swamy; Ajit Singh Nain

    2014-01-01

    The purpose of this study was to characterize the land use, vegetation structure, and diversity in the Barnowpara Sanctuary, Raipur district, Chhattisgarh, India through the use of satellite remote sensing and GIS. Land cover and vegetation were spatially analyzed by digitally classifying IRS 1D LISS III satellite data using a maximum likelihood algorithm. Later, the variations in structure and diversity in different forest types and classes were quantified by adopting quadratic sampling proce-dures. Nine land-cover types were delineated: teak forest, dense mixed forest, degraded mixed forest, Sal mixed forest, open mixed forest, young teak plantation, grasslands, agriculture, habitation, and water bodies. The classification accuracy for different land-use classes ranged from 71.23%to 100%. The highest accuracy was observed in water bodies and grass-land, followed by habitation and agriculture, teak forest, degraded mixed forest, and dense mixed forest. The accuracy was lower in open mixed forest, and sal mixed forest. Results revealed that density of different forest types varied from 324 to 733 trees ha-1, basal area from 8.13 to 28.87 m2·ha-1 and number of species from 20 to 40. Similarly, the diversity ranged from 1.36 to 2.98, concentration of dominance from 0.06 to 0.49, species richness from 3.88 to 6.86, and beta diversity from 1.29 to 2.21. The sal mixed forest type recorded the highest basal area, diversity was highest in the dense mixed forest, and the teak forest recorded maximum density, which was poor in degraded mixed forests. The study also showed that Normalized Difference Vegetation Index (NDVI) was strongly cor-related to with the Shannon Index and species richness.

  7. Genetic diversity and differentiation in roses: A gardenrose perspective

    NARCIS (Netherlands)

    Vukosavljev, M.; Zhang, J.; Esselink, G.; Westende, van 't W.P.C.; Cox, P.; Visser, R.G.F.; Arens, P.; Smulders, M.J.M.

    2013-01-01

    tFor the first time genetic diversity among modern garden rose cultivars has been evaluated using a setof 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtainedin the set of 138 rose cultivars and this led to the conclusion that in terms of genetic

  8. Genetic diversity of Toxoplama gondii isolates from Ethiopian feral cats

    Science.gov (United States)

    Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioa...

  9. Original Paper Patterns of genetic structure and phenotypic diversity ...

    African Journals Online (AJOL)

    Patterns of genetic structure and phenotypic diversity in sorghum landraces in relation to farmers' management in Burkina Faso ... the role of farmer practices in phenotypic and genetic evolution of sorghum. ... varieties to marginal environments such as ...... Supporting the Convention on Biological ... A new method to.

  10. Genetic diversity and demographic evolution of baobab (Adansonia ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2013-09-18

    Sep 18, 2013 ... This study evaluated the spatial genetic structure of baobab ... digitata, haplotype, genetic diversity, demographic evolution. ... use in domestication, conservation, management and .... Benin, and inferred some impact of the environment and ... new diploid species from Africa, which co-exists with A.

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

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... diversity and genetic structure of 35 maize accessions using 10 microsatellite markers. These accessions ... In addition, they provide new sources of resistance to ..... http://taylor0.biology.ucla.edu/structureHarvester/.The .... environment and in other areas. ..... Molecular population genetics and evolution. In:.

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

    African Journals Online (AJOL)

    fire7-

    2016-12-28

    Dec 28, 2016 ... markers to assess the genetic diversity within and between common bean landraces, classifying them based on ... since the 1980's from continuous introduction of new ... control genotypes for the Andean and Mesoamerican gene pools, ... http://biology.anu.edu.au/GenAlEx/) was used to calculate genetic.

  13. Genetic diversity in green gram [Vigna radiata (L.)] landraces ...

    African Journals Online (AJOL)

    GRACE

    2006-07-03

    Jul 3, 2006 ... Sciences, School of Biological Sciences, Madurai Kamaraj University, ... Nadu, India, to determine the extent of genetic diversity at DNA level by random amplified polymorphic ... evolutionary forces such as natural selection and genetic ... supernatant was transferred to a new centrifuge tube, and 0.7.

  14. Assessment of the genetic diversity and pattern of relationship of ...

    African Journals Online (AJOL)

    SAM

    2014-04-02

    Apr 2, 2014 ... the hierarchical partitioning of genetic variation by AMOVA demonstrated ... sorghum using both phenotypic and molecular markers ... tained population breeding and hybrid development in ... countries and diverse geographic origins in West Africa and their ...... Evolution and the genetics of populations Vol.

  15. Study of genetic diversity in finger millet (Eleusine coracana L ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... portions of genome, and detects evolutionary homologous changes. ... using these data either to estimate genetic variation present within and ... Development costs ..... possibility of linkage with an area of specific phenotype. Presence of .... Assessment of genome origins and genetic diversity in the genus.

  16. Genetic diversity analysis of pearl millet (Pennisetum glauccum [L ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-16

    Nov 16, 2009 ... Random amplified polymorphic DNA (RAPD) analysis was applied ... ding reliable information for the calculation of genetic dis- tance and pedigree studies. Thus, for genetic diversity assessment, molecular markers offer considerable ad- .... morphism (%) = total number of bands - number of monomorphic.

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

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... positive correlation between molecular genetic variation and actual population size. ... Key words: Capparis decidua, Tandhab, Assos, Population size, RAPD markers, Genetic diversity. .... polymorphism in some population, and were monomorphic ... highly informative and produced 152 bands with an ...

  18. Assessment of genetic diversity within sour cherry clones

    DEFF Research Database (Denmark)

    Clausen, S. K.; Andersen, S. B.; Henriksen, K.;

    2013-01-01

    of improved breeding material. However, no differences in allele profile were found between or within the clones, calling into question the extent of the available genetic diversity and indicating that the observed variance in yield may have to be explained by other genetic mechanisms, including epigenetic...

  19. Conserving the genetic diversity of Bolivian wild potatoes

    NARCIS (Netherlands)

    Cadima Fuentes, X.

    2014-01-01

    Abstract thesis Ximena Cadima Fuentes (to be defended on 8 Dec 2014): Conserving the genetic diversity of Bolivian wild potatoes The wild relatives of potatoes (Solanum sect. Petota) form the genetic reservoir for the improvement of the cultivated

  20. Diversity and composition of herbaceous angiosperms along gradients of elevation and forest-use intensity.

    Science.gov (United States)

    Gómez-Díaz, Jorge Antonio; Krömer, Thorsten; Kreft, Holger; Gerold, Gerhard; Carvajal-Hernández, César Isidro; Heitkamp, Felix

    2017-01-01

    Terrestrial herbs are important elements of tropical forests; however, there is a lack of research on their diversity patterns and how they respond to different intensities of forest-use. The aim of this study was to analyze the diversity of herbaceous angiosperms along gradients of elevation (50 m to 3500 m) and forest-use intensity on the eastern slopes of the Cofre de Perote, Veracruz, Mexico. We recorded the occurrence of all herbaceous angiosperm species within 120 plots of 20 m x 20 m each. The plots were located at eight study locations separated by ~500 m in elevation and within three different habitats that differ in forest-use intensity: old-growth, degraded, and secondary forest. We analyzed species richness and floristic composition of herb communities among different elevations and habitats. Of the 264 plant species recorded, 31 are endemic to Mexico. Both α- and γ-diversity display a hump-shaped relation to elevation peaking at 2500 m and 3000 m, respectively. The relative contribution of between-habitat β-diversity to γ-diversity also showed a unimodal hump whereas within-habitat β-diversity declined with elevation. Forest-use intensity did not affect α-diversity, but β-diversity was high between old-growth and secondary forests. Overall, γ-diversity peaked at 2500 m (72 species), driven mainly by high within- and among-habitat β-diversity. We infer that this belt is highly sensitive to anthropogenic disturbance and forest-use intensification. At 3100 m, high γ-diversity (50 species) was driven by high α- and within-habitat β-diversity. There, losing a specific forest area might be compensated if similar assemblages occur in nearby areas. The high β-diversity and endemism suggest that mixes of different habitats are needed to sustain high γ-richness of terrestrial herbs along this elevational gradient.

  1. Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

    Directory of Open Access Journals (Sweden)

    Binu M Tripathi

    2016-04-01

    Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

  2. Rapid Increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests.

    Science.gov (United States)

    Pec, Gregory J; Karst, Justine; Sywenky, Alexandra N; Cigan, Paul W; Erbilgin, Nadir; Simard, Suzanne W; Cahill, James F

    2015-01-01

    The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.

  3. Rapid Increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae outbreak in pine forests.

    Directory of Open Access Journals (Sweden)

    Gregory J Pec

    Full Text Available The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae in lodgepole pine (Pinus contorta forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.

  4. tree structural and species diversities in okwangwo forest, cross river ...

    African Journals Online (AJOL)

    Tersor

    For sound forest management decisions, appraisal of flora species and forest structure is crucial for any meaningful conservation work. We assessed tree species distribution in Okwangwo Forest, Nigeria. ...... Structures and Yield Models.

  5. Genetic diversity in farm animals - A review

    NARCIS (Netherlands)

    Groeneveld, L. F.; Lenstra, J. A.; Eding, H.; Toro, M. A.; Scherf, B.; Pilling, D.; Negrini, R.; Finlay, E. K.; Jianlin, H.; Groeneveld, E.; Weigend, S.

    2010-01-01

    Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, m

  6. The intermediate disturbance hypothesis applies to tropical forests, but disturbance contributes little to tree diversity

    NARCIS (Netherlands)

    Bongers, F.; Poorter, L.; Hawthorne, W.D.; Sheil, D.

    2009-01-01

    The intermediate disturbance hypothesis (IDH) predicts local species diversity to be maximal at an intermediate level of disturbance. Developed to explain species maintenance and diversity patterns in species-rich ecosystems such as tropical forests, tests of IDH in tropical forest remain scarce, sm

  7. History and conservation of wild and cultivated plant diversity in Uganda: Forest species and banana varieties as case studies

    Directory of Open Access Journals (Sweden)

    Alan C. Hamilton

    2016-02-01

    Full Text Available The history of wild and cultivated plant diversity in Uganda is reviewed, taking forest species and bananas as examples. Palynological research into past human influences on forests is reassessed. The evidence suggests that crops were first introduced into the country at about 1000 BCE, farming communities practicing slash and burn agriculture started to significantly influence the floristic composition of forests during the 1st millennium BCE and there was a major episode of forest reduction at about 1000 CE related to socio-economic change. Bananas were probably introduced in the early centuries CE. The colonial era from 1894 saw the introduction of new concepts of land ownership and the establishment of forest reserves and agricultural stations. Forests and banana diversity are currently under threat, Uganda having a very high rate of deforestation and endemic banana varieties proving susceptible to introduced pests and diseases. It is suggested that, under these circumstances, conservationists take an opportunistic approach to field engagement, making use of favourable local conditions as they arise. Partnerships should be sought with elements of society concerned with sustainable use, provision of ecosystem services and cultural survival to widen the social base of plant conservation. International organisations involved in conservation of plant genetic resources and wild plant species should collaborate with one another to develop the conceptual basis of plant conservation, to make it more relevant to countries like Uganda.

  8. Benefits of host genetic diversity for resistance to infection depend on parasite diversity.

    Science.gov (United States)

    Ganz, Holly H; Ebert, Dieter

    2010-05-01

    Host populations with high genetic diversity are predicted to have lower levels of infection prevalence. This theory assumes that host genetic diversity results in variation in susceptibility and that parasites exhibit variation in infectivity. Empirical studies on the effects of host heterogeneity typically neglect the role of parasite diversity. We conducted three laboratory experiments designed to test if genetic variation in Daphnia magna populations and genetic variation in its parasites together influence the course of parasite spread after introduction. We found that a natural D. magna population exhibited variation in susceptibility to infection by three parasite species and had strong host clone-parasite species interactions. There was no effect of host heterogeneity in experimental host populations (polycultures and monocultures) separately exposed to single strains of three parasite species. When we manipulated the genetic diversity of a single parasite species and exposed them to host monocultures and polycultures, we found that parasite prevalence increased with the number of parasite strains. Host monocultures exposed to several parasite strains had higher mean parasite prevalence and higher variance than polycultures. These results indicate that effect of host genetic diversity on the spread of infection depends on the level of genetic diversity in the parasite population.

  9. Pollen flow in fragmented landscapes maintains genetic diversity following stand-replacing disturbance in a neotropical pioneer tree, Vochysia ferruginea Mart.

    Science.gov (United States)

    Davies, S J; Cavers, S; Finegan, B; White, A; Breed, M F; Lowe, A J

    2015-08-01

    In forests with gap disturbance regimes, pioneer tree regeneration is typically abundant following stand-replacing disturbances, whether natural or anthropogenic. Differences in pioneer tree density linked to disturbance regime can influence pollinator behaviour and impact on mating patterns and genetic diversity of pioneer populations. Such mating pattern shifts can manifest as higher selfing rates and lower pollen diversity in old growth forest populations. In secondary forest, where more closely related pollen donors occur, an increase in biparental inbreeding is a potential problem. Here, we investigate the consequences of secondary forest colonisation on the mating patterns and genetic diversity of open-pollinated progeny arrays for the long-lived, self-compatible pioneer tree, Vochysia ferruginea, at two Costa Rican sites. Five microsatellite loci were screened across adult and seed cohorts from old growth forest with lower density, secondary forest with higher density, and isolated individual trees in pasture. Progeny from both old growth and secondary forest contexts were predominantly outcrossed (tm=1.00) and experienced low levels of biparental inbreeding (tm-ts=0.00-0.04). In contrast to predictions, our results indicated that the mating patterns of V. ferruginea are relatively robust to density differences between old growth and secondary forest stands. In addition, we observed that pollen-mediated gene flow possibly maintained the genetic diversity of open-pollinated progeny arrays in stands of secondary forest adults. As part of a natural resource management strategy, we suggest that primary forest remnants should be prioritised for conservation to promote restoration of genetic diversity during forest regeneration.

  10. Fungal disease incidence along tree diversity gradients depends on latitude in European forests

    OpenAIRE

    Nguyen, Diem; Castagneyrol, Bastien; Bruelheide, Helge; Bussotti, Filippo; Guyot, Virginie; Jactel, Hervé; Jaroszewicz, Bogdan; Valladares, Fernando; Stenlid, Jan; Boberg, Johanna

    2016-01-01

    International audience; European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree speci...

  11. Hitchhiker's guide to genetic diversity in socially structured populations

    Institute of Scientific and Technical Information of China (English)

    L.S.PREMO

    2012-01-01

    When selection increases the frequency of a beneficial gene substitution it can also increase the frequencies of linked neutral alleles through a process called genetic hitchhiking.A model built to investigate reduced genetic diversity in Pleistocene hominins shows that genetic hitchhiking can have a strong effect on neutral diversity in the presence of culturally mediated migration.Under conditions in which genetic and cultural variants are transmitted symmetrically,neutral genes may also hitchhike to higher frequencies on the coattails of adaptive cultural traits through a process called cultural hitchhiking.Cultural hitchhiking has been proposed to explain why some species of matrilineal whales display relatively low levels of mitochondrial DNA diversity,and it may be applicable to humans as well.This paper provides a critical review of recent models of both types of hitchhiking in socially structured populations.The models' assumptions and predictions are compared and discussed in the hope that studies of reduced genetic diversity in humans might improve our understanding of reduced genetic diversity in other species,and vice versa [Current Zoology 58 (1):287-297,2012].

  12. Bamboo: an overview on its genetic diversity and characterization.

    Science.gov (United States)

    Yeasmin, Lucina; Ali, Md Nasim; Gantait, Saikat; Chakraborty, Somsubhra

    2015-02-01

    Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.

  13. 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

    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. PMID:24260149

  14. 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.

  15. Forest Productivity and Diversity: Using Ecological Theory and Landscape Models to Guide Sustainable Forest Management

    Energy Technology Data Exchange (ETDEWEB)

    Huston, M.A.

    1998-11-01

    Sustainable forest management requires maintaining or increasing ecosystem productivity, while preserving or restoring natural levels of biodiversity. Application of general concepts from ecological theory, along with use of mechanistic, landscape-based computer models, can contribute to the successful achievement of both of these objectives. Ecological theories based on the energetics and dynamics of populations can be used to predict the general distribution of individual species, the diversity of different types of species, ecosystem process rates and pool sizes, and patterns of spatial and temporal heterogeneity over a broad range of environmental conditions. This approach requires subdivision of total biodiversity into functional types of organisms, primarily because different types of organisms respond very differently to the spatial and temporal variation of environmental conditions on landscapes. The diversity of species of the same functional type (particularly among plants) tends to be highest at relatively low levels of net primary productivity, while the total number of different functional types (particularly among animals) tends to be highest at high levels of productivity (e.g., site index or potential net primary productivity). In general, the diversity of animals at higher trophic levels (e.g., predators) reaches its maximum at much higher levels of productivity than the diversity of lower trophic levels (e.g., plants). This means that a single environment cannot support high diversity of all types of organisms. Within the framework of the general patterns described above, the distributions, population dynamics, and diversity of organisms in specific regions can be predicted more precisely using a combination of computer simulation models and GIS data based on satellite information and ground surveys. Biophysical models that use information on soil properties, climate, and hydrology have been developed to predict how the abundance and spatial

  16. Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

    Science.gov (United States)

    Santos, Bráulio A; Arroyo-Rodríguez, Víctor; Moreno, Claudia E; Tabarelli, Marcelo

    2010-09-08

    Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

  17. Does the Transfer of Forest Reproductive Material Significantly Affect Local Tree Diversity?

    NARCIS (Netherlands)

    Kramer, K.; Geburek, Thomas; Jansen, Simon

    2016-01-01

    Genetic variation within tree species is an important component
    of forest biodiversity. It enables forest ecosystems to adapt to
    environmental changes and it provides genetic material for
    breeding to sustainably increase production. In the framework of
    forestry activities, tree

  18. Genetic patterns in forest antelope populations in the Udzungwa Mountains, Tanzania, as inferred from non-invasive sampling

    DEFF Research Database (Denmark)

    Bowkett, Andrew E.; Jones, Trevor; Rovero, Francesco

    2015-01-01

    As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution, intraspec...... except the endangered C. spadix. Overall, our results demonstrate the value of non-invasive genetic sampling in studying the distribution and evolution of rarely observed species.......As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution......, intraspecific diversity and population subdivision within the Udzungwa landscape. Most species were detected in the majority of forest fragments, except for Philantomba monticola. Phylogenetic analyses were consistent with traditional taxonomy with the exception of Cephalophus harveyi which was paraphyletic...

  19. Genetic Diversity among Ancient Nordic Populations

    DEFF Research Database (Denmark)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R;

    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...

  20. 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.

  1. [Evolutionary process unveiled by the maximum genetic diversity hypothesis].

    Science.gov (United States)

    Huang, Yi-Min; Xia, Meng-Ying; Huang, Shi

    2013-05-01

    As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature.

  2. Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes.

    Science.gov (United States)

    Napolitano, Constanza; Díaz, Diego; Sanderson, Jim; Johnson, Warren E; Ritland, Kermit; Ritland, Carol E; Poulin, Elie

    2015-01-01

    Landscape fragmentation is often a major cause of species extinction as it can affect a wide variety of ecological processes. The impact of fragmentation varies among species depending on many factors, including their life-history traits and dispersal abilities. Felids are one of the groups most threatened by fragmented landscapes because of their large home ranges, territorial behavior, and low population densities. Here, we model the impacts of habitat fragmentation on patterns of genetic diversity in the guigna (Leopardus guigna), a small felid that is closely associated with the heavily human-impacted temperate rainforests of southern South America. We assessed genetic variation in 1798 base pairs of mitochondrial DNA sequences, 15 microsatellite loci, and 2 sex chromosome genes and estimated genetic diversity, kinship, inbreeding, and dispersal in 38 individuals from landscapes with differing degrees of fragmentation on Chiloé Island in southern Chile. Increased fragmentation was associated with reduced genetic diversity, but not with increased kinship or inbreeding. However, in fragmented landscapes, there was a weaker negative correlation between pairwise kinship and geographic distance, suggesting increased dispersal distances. These results highlight the importance of biological corridors to maximize connectivity in fragmented landscapes and contribute to our understanding of the broader genetic consequences of habitat fragmentation, especially for forest-specialist carnivores.

  3. 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...

  4. Ensuring the genetic diversity of potatoes

    Science.gov (United States)

    Opportunities for advances in the potato crop through genetics are great, since potato has many needs for improvement, and many related species with the traits required are available. Genebanks provide a centralized and specialized resource for providing the services of acquisition, classification, ...

  5. [Genetic diversity of eukaryotic picoplankton of eight lakes in Nanjing].

    Science.gov (United States)

    Zhao, Bi-ying; Chen, Mei-jun; Sun, Ying; Chen, Fei-zhou; Yang, Jia-xin

    2010-05-01

    The method of terminal restriction fragment length polymorphism (T-RFLP) was used to study the genetic diversity of eukaryotic picoplankton (0.2-5.0 microm) in the pelagic and littoral zones in 8 lakes with different trophic status in Nanjing. The objectives of this study were to confirm the difference of the genetic diversity of eukaryotic picoplankton among lakes and the main factors affecting this difference. T-RFLP indicated that there were various fingerprints among lakes and zones. The average terminal restriction fragments (T-RFs) in the littoral and pelagic zones were 16.4 and 15.9, respectively. The littoral zone in Lake Nan and the pelagic zone in Lake Mochou had 30 T-RFs and 27 T-RFs, respectively. The T-RFs were the least abundant (10) in the pelagic zone in Lake Baijia with relatively low trophic status. The genetic diversity of eukaryotic picoplankton was higher in the littoral zone than that in the pelagic zone except Lake Pipa and Mochou. The cluster analysis indicated that the similarities of the littoral zones and the pelagic zones were very high except Lake Baijia, Qian and Nan. The canonical correspondence analysis between the genetic diversity of eukaryotic picoplankton and environmental factors revealed the concentration of chlorophyll a had the most important impact on the eukaryotic picoplankton communities (p = 0.004). The results indicated that the genetic diversity of eukaryotic picoplankton is affected by the trophic status and has the difference in the pelagic and littoral zones.

  6. Genetic diversity and gene flow in the morphologically variable, rare endemics Begonia dregei and Begonia homonyma (Begoniaceae).

    Science.gov (United States)

    Matolweni, L O; Balkwill, K; McLellan, T

    2000-03-01

    Begonia dregei and B. homonyma (Begoniaceae), rare plants endemic to coastal forests of eastern South Africa, are two closely related species with high levels of variation among populations in the shape of leaves. Distribution of genetic variation and genetic relatedness were investigated in 12 populations of B. dregei and seven of B. homonyma using polyacrylamide gel electrophoresis. Twelve of the 15 enzyme loci examined were polymorphic, but only seven loci were polymorphic within at least one population. Genetic diversity measures indicated that the among-population gene differentiation represents >90% of the total genetic component in both species considered individually or combined. This indicated restricted gene flow, consistent with the limited dispersal abilities of Begonia generally and the ancient separation of isolated forest patches. Genetic distances among populations are much higher than usually found within species. Allozyme data provide no support for the recognition of B. dregei and B. homonyma as distinct species.

  7. Genetic diversity in Hemileia vastatrix based on RAPD markers.

    Science.gov (United States)

    Gouveia, M Manuela C; Ribeiro, Ana; Várzea, Vítor M P; Rodrigues, Carlos J

    2005-01-01

    Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs.

  8. Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest.

    Science.gov (United States)

    Slik, J W Ferry; Bernard, Caroline S; Van Beek, Marloes; Breman, Floris C; Eichhorn, Karl A O

    2008-12-01

    Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur more frequently and at larger spatial scales than they used to. We studied forest structure, tree species diversity, tree species composition, and aboveground biomass during the first 7 years since fire in unburned, once burned and twice burned forest of eastern Borneo to determine the rate of recovery of these forests. We paid special attention to changes in the tree species composition during burned forest regeneration because we expect the long-term recovery of aboveground biomass and ecosystem functions in burned forests to largely depend on the successful regeneration of the pre-fire, heavy-wood, species composition. We found that forest structure (canopy openness, leaf area index, herb cover, and stem density) is strongly affected by fire but shows quick recovery. However, species composition shows no or limited recovery and aboveground biomass, which is greatly reduced by fire, continues to be low or decline up to 7 years after fire. Consequently, large amounts of the C released to the atmosphere by fire will not be recaptured by the burned forest ecosystem in the near future. We also observed that repeated fire, with an inter-fire interval of 15 years, does not necessarily lead to a huge deterioration in the regeneration potential of tropical forest. We conclude that burned forests are valuable and should be conserved and that long-term monitoring programs in secondary forests are necessary to determine their recovery rates, especially in relation to aboveground biomass accumulation.

  9. Human Influences on Tree Diversity and Composition of a Coastal Forest Ecosystem: The Case of Ngumburuni Forest Reserve, Rufiji, Tanzania

    Directory of Open Access Journals (Sweden)

    J. Kimaro

    2013-01-01

    Full Text Available This paper reports on the findings of an ecological survey conducted in Ngumburuni Forest Reserve, a biodiversity rich forest reserve within the coastal forests of Tanzania. The main goal of this study was to determine the influence of uncontrolled anthropogenic activities on tree species diversity and composition within the forest ecosystem. It was revealed that economic activities including logging, charcoaling, and shifting cultivation were the most important disturbing activities affecting ecological functioning and biodiversity integrity of the forest. Further to this, we noted that the values of species diversity, composition, and regeneration potential within the undisturbed forest areas were significantly different from those in heavily disturbed areas. These observations confirm that the ongoing human activities have already caused size quality degradation of useful plants, enhanced species diversification impacts to the forest ecosystem, and possibly negatively affected the livelihoods of the adjacent local communities. Despite these disturbances, Ngumburuni forest reserve still holds important proportions of both endemic and threatened animal and plant species. The study suggests urgent implementation of several conservation measures in order to limit accessibility to the forest resources so as to safeguard the richness and abundance of useful biodiversity stocks in the reserve.

  10. Plant genetics. Ancient wild olives in Mediterranean forests.

    Science.gov (United States)

    Lumaret, R; Ouazzani, N

    2001-10-18

    Early domestication and extensive cultivation have meant that staple Mediterranean fruit crops such as olives, grapes and dates exist in wild-looking forms that are secondary derivatives produced by sexual reproduction among cultivated plants (cultivars), which were initially propagated vegetatively. By using genetic markers associated with characters that render plants unsuitable for domestication, we show here that genuinely wild olive trees, which cannot be distinguished morphologically from feral forms, still survive in a few Mediterranean forests. These wild stocks are genetically distinct and more variable than either the crop strains or their derived feral forms, a finding that has important implications for the conservation of these ancient lineages.

  11. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

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

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however......, 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...... locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among...

  12. Research and Conservation of Forest Genetic Resources in China

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The present situation of forest tree genetic germplasm resources research and conservation in China is introduced which including the background, decision-making of conservation strategies and principles, the plan of area division and tree species classification, the sample strategy of germplasm conservation, the advances in conservation pattern and related technologies research, the achievements of germplasm conservation and utilization in China, and the problems to be solved. The recent achievements a...

  13. SSR Analysis of Genetic Diversity Among 192 Diploid Potato Cultivars

    Directory of Open Access Journals (Sweden)

    Xiaoyan Song

    2016-05-01

    Full Text Available In potato breeding, it is difficult to improve the traits of interest at the tetraploid level due to the tetrasomic inheritance. A promising alternative is diploid breeding. Thus it is necessary to assess the genetic diversity of diploid potato germplasm for efficient exploration and deployment of desirable traits. In this study, we used SSR markers to evaluate the genetic diversity of diploid potato cultivars. To screen polymorphic SSR markers, 55 pairs of SSR primers were employed to amplify 39 cultivars with relatively distant genetic relationships. Among them, 12 SSR markers with high polymorphism located at 12 chromosomes were chosen to evaluate the genetic diversity of 192 diploid potato cultivars. The primers produced 6 to 18 bands with an average of 8.2 bands per primer. In total, 98 bands were amplified from 192 cultivars, and 97 of them were polymorphic. Cluster analysis using UPGMA showed the genetic relationships of all accessions tested: 186 of the 192 accessions could be distinguished by only 12 pairs of SSR primers, and the 192 diploid cultivars were divided into 11 groups, and 83.3% constituted the first group. Clustering results showed relatively low genetic diversity among 192 diploid cultivars, with closer relationship at the molecular level. The results can provide molecular basis for diploid potato breeding.

  14. Genetic diversity among ancient Nordic populations.

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, 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 locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  15. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  16. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  17. Genetic diversity analysis of common beans based on molecular markers

    Science.gov (United States)

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  18. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  19. Loss of functional diversity of ant assemblages in secondary tropical forests.

    Science.gov (United States)

    Bihn, Jochen H; Gebauer, Gerhard; Brandl, Roland

    2010-03-01

    Secondary forests and plantations increasingly dominate the tropical wooded landscape in place of primary forests. The expected reduction of biodiversity and its impact on ecological functions provided by these secondary forests are of major concern to society and ecologists. The potential effect of biodiversity loss on ecosystem functioning depends largely on the associated loss in the functional diversity of animal and plant assemblages, i.e., the degree of functional redundancy among species. However, the relationship between species and functional diversity is still poorly documented for most ecosystems. Here, we analyze how changes in the species diversity of ground-foraging ant assemblages translate into changes of functional diversity along a successional gradient of secondary forests in the Atlantic Forest of Brazil. Our analysis uses continuous measures of functional diversity and is based on four functional traits related to resource use of ants: body size, relative eye size, relative leg length, and trophic position. We find a strong relationship between species and functional diversity, independent of the functional traits used, with no evidence for saturation in this relationship. Recovery of species richness and diversity of ant assemblages in tropical secondary forests was accompanied by a proportional increase of functional richness and diversity of assemblages. Moreover, our results indicate that the increase in functional diversity along the successional gradient of secondary forests is primarily driven by rare species, which are functionally unique. The observed loss of both species and functional diversity in secondary forests offers no reason to believe that the ecological functions provided by secondary forests are buffered against species loss through functional redundancy.

  20. Tree diversity does not always improve resistance of forest ecosystems to drought.

    Science.gov (United States)

    Grossiord, Charlotte; Granier, André; Ratcliffe, Sophia; Bouriaud, Olivier; Bruelheide, Helge; Chećko, Ewa; Forrester, David Ian; Dawud, Seid Muhie; Finér, Leena; Pollastrini, Martina; Scherer-Lorenzen, Michael; Valladares, Fernando; Bonal, Damien; Gessler, Arthur

    2014-10-14

    Climate models predict an increase in the intensity and frequency of drought episodes in the Northern Hemisphere. Among terrestrial ecosystems, forests will be profoundly impacted by drier climatic conditions, with drastic consequences for the functions and services they supply. Simultaneously, biodiversity is known to support a wide range of forest ecosystem functions and services. However, whether biodiversity also improves the resistance of these ecosystems to drought remains unclear. We compared soil drought exposure levels in a total of 160 forest stands within five major forest types across Europe along a gradient of tree species diversity. We assessed soil drought exposure in each forest stand by calculating the stand-level increase in carbon isotope composition of late wood from a wet to a dry year (Δδ(13)CS). Δδ(13)CS exhibited a negative linear relationship with tree species diversity in two forest types, suggesting that species interactions in these forests diminished the drought exposure of the ecosystem. However, the other three forest types were unaffected by tree species diversity. We conclude that higher diversity enhances resistance to drought events only in drought-prone environments. Managing forest ecosystems for high tree species diversity does not necessarily assure improved adaptability to the more severe and frequent drought events predicted for the future.

  1. Fungal disease incidence along tree diversity gradients depends on latitude in European forests.

    Science.gov (United States)

    Nguyen, Diem; Castagneyrol, Bastien; Bruelheide, Helge; Bussotti, Filippo; Guyot, Virginie; Jactel, Hervé; Jaroszewicz, Bogdan; Valladares, Fernando; Stenlid, Jan; Boberg, Johanna

    2016-04-01

    European forests host a diversity of tree species that are increasingly threatened by fungal pathogens, which may have cascading consequences for forest ecosystems and their functioning. Previous experimental studies suggest that foliar and root pathogen abundance and disease severity decrease with increasing tree species diversity, but evidences from natural forests are rare. Here, we tested whether foliar fungal disease incidence was negatively affected by tree species diversity in different forest types across Europe. We measured the foliar fungal disease incidence on 16 different tree species in 209 plots in six European countries, representing a forest-type gradient from the Mediterranean to boreal forests. Forest plots of single species (monoculture plots) and those with different combinations of two to five tree species (mixed species plots) were compared. Specifically, we analyzed the influence of tree species richness, functional type (conifer vs. broadleaved) and phylogenetic diversity on overall fungal disease incidence. The effect of tree species richness on disease incidence varied with latitude and functional type. Disease incidence tended to increase with tree diversity, in particular in northern latitudes. Disease incidence decreased with tree species richness in conifers, but not in broadleaved trees. However, for specific damage symptoms, no tree species richness effects were observed. Although the patterns were weak, susceptibility of forests to disease appears to depend on the forest site and tree type.

  2. Genetic Diversity in the Interference Selection Limit

    Science.gov (United States)

    Good, Benjamin H.; Walczak, Aleksandra M.; Neher, Richard A.; Desai, Michael M.

    2014-01-01

    Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics fails to account for interference between linked mutations, which grows increasingly severe as the density of selected polymorphisms increases. Here, we describe a simple limit that emerges when interference is common, in which the fitness effects of individual mutations play a relatively minor role. Instead, similar to models of quantitative genetics, molecular evolution is determined by the variance in fitness within the population, defined over an effectively asexual segment of the genome (a “linkage block”). We exploit this insensitivity in a new “coarse-grained” coalescent framework, which approximates the effects of many weakly selected mutations with a smaller number of strongly selected mutations that create the same variance in fitness. This approximation generates accurate and efficient predictions for silent site variability when interference is common. However, these results suggest that there is reduced power to resolve individual selection pressures when interference is sufficiently widespread, since a broad range of parameters possess nearly identical patterns of silent site variability. PMID:24675740

  3. Vietnamese chickens: a gate towards Asian genetic diversity

    Directory of Open Access Journals (Sweden)

    Bed'Hom B

    2010-06-01

    Full Text Available Abstract Background Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. Results A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69. The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. Conclusions

  4. Tree diversity does not always improve resistance of forest ecosystems to drought

    DEFF Research Database (Denmark)

    Grossiord, Charlotte; Granier, André; Ratcliffe, Sophia

    2014-01-01

    , biodiversity is known to support a wide range of forest ecosystem functions and services. However, whether biodiversity also improves the resistance of these ecosystems to drought remains unclear. We compared soil drought exposure levels in a total of 160 forest stands within five major forest types across...... in two forest types, suggesting that species interactions in these forests diminished the drought exposure of the ecosystem. However, the other three forest types were unaffected by tree species diversity. We conclude that higher diversity enhances resistance to drought events only in drought......Climate models predict an increase in the intensity and frequency of drought episodes in the Northern Hemisphere. Among terrestrial ecosystems, forests will be profoundly impacted by drier climatic conditions, with drastic consequences for the functions and services they supply. Simultaneously...

  5. EUFORGEN as an instrument for the conservation of European forest genetic resources

    NARCIS (Netherlands)

    Vries, de S.M.G.

    2006-01-01

    Following the Ministerial Conference for the Protection of Forest in Europe, held in Strasbourg in 1990, and more specifically its Resolution No. 2 concerning the conservation of forest genetic resources EUFORGEN (European Forest Genetic Resources Programme) was established. EUFORGEN is a collaborat

  6. EUFORGEN as an instrument for the conservation of European forest genetic resources

    NARCIS (Netherlands)

    Vries, de S.M.G.

    2006-01-01

    Following the Ministerial Conference for the Protection of Forest in Europe, held in Strasbourg in 1990, and more specifically its Resolution No. 2 concerning the conservation of forest genetic resources EUFORGEN (European Forest Genetic Resources Programme) was established. EUFORGEN is a

  7. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, 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 locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  8. Diversity of Ancient Woody Species in Urban Forests

    Directory of Open Access Journals (Sweden)

    Fornal-Pieniak Beata

    2014-06-01

    Full Text Available Mostly parks and forest are the most important ‘green islands’ in urban ecological network. Urban forests are belong to green areas and collected many plant species. The main aim of the article was characteristic of ancient plant species in urban forests in Tarnów. The field studies were carried out in years 2011-2012. It covered 80 phytosociological records on the area 500 m2 in herb layer of urban forests and in forest nature on oak-hornbeam. The results showed that many ancient plant species were growing in urban forest but less than in nature reserves

  9. The Forest Genetic Resources Working Group of the North American Forestry Commission (FAO)

    Science.gov (United States)

    Ronald C. Schmidtling

    2002-01-01

    The Forest Genetic Resources Working Group (FGRWG) is one of seven working groups established by the North American Forest Commission (NAFC). The NAFC is one of six Forest Commissions established by the Food and Agriculture Organization (F-40). The FGRWG was established by the NAFC in 1961 as the Working Group on Forest Tree Improvement but went through several-changes...

  10. Diversity-Oriented Synthesis as a Tool for Chemical Genetics

    Directory of Open Access Journals (Sweden)

    Elena Lenci

    2014-10-01

    Full Text Available Chemical genetics is an approach for identifying small molecules with the ability to induce a biological phenotype or to interact with a particular gene product, and it is an emerging tool for lead generation in drug discovery. Accordingly, there is a need for efficient and versatile synthetic processes capable of generating complex and diverse molecular libraries, and Diversity-Oriented Synthesis (DOS of small molecules is the concept of choice to give access to new chemotypes with high chemical diversity. In this review, the combination of chemical genetics and diversity-oriented synthesis to identify new chemotypes as hit compounds in chemical biology and drug discovery is reported, giving an overview of basic concepts and selected case studies.

  11. Genetic Diversity Based on Allozyme Alleles of Chinese Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    TANG Sheng-xiang; WEI Xing-hua; JIANG Yun-zhu; D S Brar; G S Khush

    2007-01-01

    Genetic diversity was analyzed with 6 632 core rice cultivars selected from 60 282 Chinese rice accessions on the basis of 12 allozyme loci, Pgil, Pgi2, Ampl, Amp2, Amp3, Amp4, Sdh1, Adh1, Est1, Est2, Est5 and Est9, by starch gel electrophoresis. Among the materials examined, 52 alleles at 12 polymorphic loci were identified, which occupied 96.3% of 54 alleles found in cultivated germplasm of O.sativa L. The number of alleles per locus ranged from 2 to 7 with an average of 4.33. The gene diversity (He) each locus varied considerably from 0.017 for Amp4 to 0.583 for Est2 with an average gene diversity (Ht) 0.271, and Shannon-Wiener index from 0.055 to 0.946 with an average of 0.468. The degree of polymorphism (DP) was in a range from 0.9 to 46.9% with an average of 21.4%. It was found that the genetic diversity in japonica (Keng) subspecies was lower in terms of allele's number, Ht and S-W index, being 91.8, 66.2 and 75.7% of indica (Hsien) one, respectively. Significant genetic differentiation between indica and japonica rice has been appeared in the loci Pgil, Amp2, Pgi2, and Est2, with higher average coefficient of genetic differentiation (Gst) 0.635, 0.626, 0.322 and 0.282, respectively. Except less allele number per locus (3.33) for modern cultivars, being 76.9% of landraces, the Ht and S-W index showed in similar between the modern cultivars and the landraces detected. In terms of allozyme, the rice cultivars in the Southwest Plateau and Central China have richer genetic diversity. The present study reveals again that Chinese cultivated rice germplasm has rich genetic diversity, showed by the allozyme allele variation.

  12. Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras

    Directory of Open Access Journals (Sweden)

    Lopez Ana

    2012-11-01

    Full Text Available Abstract Background Understanding the population structure of Plasmodium species through genetic diversity studies can assist in the design of more effective malaria control strategies, particularly in vaccine development. Central America is an area where malaria is a public health problem, but little is known about the genetic diversity of the parasite’s circulating species. This study aimed to investigate the allelic frequency and molecular diversity of five surface antigens in field isolates from Honduras. Methods Five molecular markers were analysed to determine the genotypes of Plasmodium vivax and Plasmodium falciparum from endemic areas in Honduras. Genetic diversity of ama-1, msp-1 and csp was investigated for P. vivax, and msp-1 and msp-2 for P. falciparum. Allelic frequencies were calculated and sequence analysis performed. Results and conclusion A high genetic diversity was observed within Plasmodium isolates from Honduras. A different number of genotypes were elucidated: 41 (n = 77 for pvama-1; 23 (n = 84 for pvcsp; and 23 (n = 35 for pfmsp-1. Pvcsp sequences showed VK210 as the only subtype present in Honduran isolates. Pvmsp-1 (F2 was the most polymorphic marker for P. vivax isolates while pvama-1 was least variable. All three allelic families described for pfmsp-1 (n = 30 block 2 (K1, MAD20, and RO33, and both allelic families described for the central domain of pfmsp-2 (n = 11 (3D7 and FC27 were detected. However, K1 and 3D7 allelic families were predominant. All markers were randomly distributed across the country and no geographic correlation was found. To date, this is the most complete report on molecular characterization of P. vivax and P. falciparum field isolates in Honduras with regards to genetic diversity. These results indicate that P. vivax and P. falciparum parasite populations are highly diverse in Honduras despite the low level of transmission.

  13. Predator diversity and abundance provide little support for the enemies hypothesis in forests of high tree diversity.

    Science.gov (United States)

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity--and thus information on the relevance of experimental findings--for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25-69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis--derived from studies in less diverse ecosystems--of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  14. Habitat fragmentation, tree diversity, and plant invasion interact to structure forest caterpillar communities.

    Science.gov (United States)

    Stireman, John O; Devlin, Hilary; Doyle, Annie L

    2014-09-01

    Habitat fragmentation and invasive species are two of the most prominent threats to terrestrial ecosystems. Few studies have examined how these factors interact to influence the diversity of natural communities, particularly primary consumers. Here, we examined the effects of forest fragmentation and invasion of exotic honeysuckle (Lonicera maackii, Caprifoliaceae) on the abundance and diversity of the dominant forest herbivores: woody plant-feeding Lepidoptera. We systematically surveyed understory caterpillars along transects in 19 forest fragments over multiple years in southwestern Ohio and evaluated how fragment area, isolation, tree diversity, invasion by honeysuckle and interactions among these factors influence species richness, diversity and abundance. We found strong seasonal variation in caterpillar communities, which responded differently to fragmentation and invasion. Abundance and richness increased with fragment area, but these effects were mitigated by high levels of honeysuckle, tree diversity, landscape forest cover, and large recent changes in area. Honeysuckle infestation was generally associated with decreased caterpillar abundance and diversity, but these effects were strongly dependent on other fragment traits. Effects of honeysuckle on abundance were moderated when fragment area, landscape forest cover and tree diversity were high. In contrast, negative effects of honeysuckle invasion on caterpillar diversity were most pronounced in fragments with high tree diversity and large recent increases in area. Our results illustrate the complex interdependencies of habitat fragmentation, plant diversity and plant invasion in their effects on primary consumers and emphasize the need to consider these processes in concert to understand the consequences of anthropogenic habitat change for biodiversity.

  15. Genetic diversity studies of Kherigarh cattle based on microsatellite markers

    Indian Academy of Sciences (India)

    A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat

    2006-08-01

    We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles were distinguished by the 21 microsatellite markers used. All the microsatellites were highly polymorphic, with mean (± s.e.) allelic number of 6.24 ± 1.7, ranging 4–10 per locus. The observed heterozygosity in the population ranged between 0.261 and 0.809, with mean (± s.e.) of 0.574 ± 0.131, indicating considerable genetic variation in this population. Genetic bottleneck hypotheses were also explored. Our data suggest that the Kherigarh breed has not experienced a genetic bottleneck in the recent past.

  16. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    OpenAIRE

    Menzies, Brandon R.; Renfree, Marilyn B; Thomas Heider; Frieder Mayer; Hildebrandt, Thomas B.; Pask, Andrew J.

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived...

  17. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    OpenAIRE

    Menzies, Brandon R; Renfree, Marilyn B.; Thomas Heider; Frieder Mayer; Thomas B. Hildebrandt; Pask, Andrew J

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived...

  18. Genetic diversity of Tricholoma matsutake in Yunnan Province

    Institute of Scientific and Technical Information of China (English)

    SHA Tao; ZHANG HanBo; DING HuaSun; LI ZongJu; CHENG LiZhong; ZHAO ZhiWei; ZHANG YaPing

    2007-01-01

    To investigate the genetic diversity of Tricholoma matsutake, we studied ITS and IGS1 sequences and PCR polymorphism of a retrotransposon in 56 fruit bodies collected from 13 counties of 9 regions in Yunnan Province. We found one and three haplotypes based on ITS and IGS1 sequences, respectively.Moreover, there was no significant difference in PCR polymorphism of the retrotransposon among different populations. Compared with Jilin Province (China) and Japanese populations, although Yunnan was highly homogenous to Japanese populations, Iow genetic diversity of T. matsutake in Yunnan did not support the view that this species originated from Yunnan.

  19. Genetic diversity analysis of fruit characteristics of hawthorn germplasm.

    Science.gov (United States)

    Su, K; Guo, Y S; Wang, G; Zhao, Y H; Dong, W X

    2015-12-07

    One hundred and six accessions of hawthorn intraspecific resources, from the National Germplasm Repository at Shenyang, were subjected to genetic diversity and principal component analysis based on evaluation data of 15 fruit traits. Results showed that the genetic diversity of hawthorn fruit traits varied. Among the 15 traits, the fruit shape variable coefficient had the most obvious evaluation, followed by fruit surface state, dot color, taste, weight of single fruit, sepal posture, peduncle form, and metula traits. These are the primary traits by which hawthorn could be classified in the future. The principal component demonstrated that these traits are the most influential factors of hawthorn fruit characteristics.

  20. Genetic diversity and breeding of larch (Larix decidua Mill. in Romania

    Directory of Open Access Journals (Sweden)

    Georgeta Mihai

    2009-12-01

    Full Text Available Although it is one of the most important coniferous species, the larch (Larix decidua Mill. covers a restricted area in Romania, only 0.3% of the forest area, most being represented by artificial stands. The natural area of the larch is fragmented, being concentrated into five genetic centers: Ceahlău, Ciucas, Bucegi, Lotru and Apuseni. The speed of growth, high productivity, high wood quality and resistance to adversities resulted in initiating research on the genetic variability of the larch. In 1978 and 1982 respectively, by means of international collaboration, two series of comparative trials were installed, with Romanian and foreign provenances of larch, totalizing 6 experimental areas. Selection of seed stands followed, and among them, more than 300 plus trees. There have been installed 26 orchards (134 hectares of which 3 (15 hectares are interspecific seed orchards (Larix x eurolepis. This paper presents the results obtained over the last years, regarding the continuing larch breeding program; genetic variation of the main characters in multisite provenances comparative trials planted in 1982, evaluation of the genetic parameters in a clonal seed orchard in order to advance to the second generation seed orchard, and a study of the genetic diversity by means of primary biochemical markers. The provenance tests include 24 populations of larch, 13 Romanian and 11 from the following countries: Germany (4, Austria (2, Belgium (1 and the Czech Republic (4. The studied characters are total height, diameter at 1.30 meters, volume/tree, branches characters, stem straightness and survival. At the age of 25 years from planting, the variance analysis reveals significant interpopulation genetic variation for all the studied characters. The expected genetic gain and the genetic parameters, estimated in the Adâncata larch seed orchard, shows that selection on the clones level, in the first generation seed orchard, can be successfully applied, being

  1. Castor bean organelle genome sequencing and worldwide genetic diversity analysis.

    Directory of Open Access Journals (Sweden)

    Maximo Rivarola

    Full Text Available Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.

  2. Castor bean organelle genome sequencing and worldwide genetic diversity analysis.

    Science.gov (United States)

    Rivarola, Maximo; Foster, Jeffrey T; Chan, Agnes P; Williams, Amber L; Rice, Danny W; Liu, Xinyue; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M J; Khouri, Hoda M; Beckstrom-Sternberg, Stephen M; Allan, Gerard J; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D

    2011-01-01

    Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.

  3. Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis

    Science.gov (United States)

    Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-Sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D.

    2011-01-01

    Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade. PMID:21750729

  4. Woody species diversity in forest plantations in a mountainous region of Beijing, China: effects of sampling scale and species selection.

    Directory of Open Access Journals (Sweden)

    Yuxin Zhang

    Full Text Available The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr., planted larch (Larix principis-rupprechtii Mayr., and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer, while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation.

  5. Bat and bird diversity along independent gradients of latitude and tree composition in European forests.

    Science.gov (United States)

    Charbonnier, Yohan M; Barbaro, Luc; Barnagaud, Jean-Yves; Ampoorter, Evy; Nezan, Julien; Verheyen, Kris; Jactel, Hervé

    2016-10-01

    Species assemblages are shaped by local and continental-scale processes that are seldom investigated together, due to the lack of surveys along independent gradients of latitude and habitat types. Our study investigated changes in the effects of forest composition and structure on bat and bird diversity across Europe. We compared the taxonomic and functional diversity of bat and bird assemblages in 209 mature forest plots spread along gradients of forest composition and vertical structure, replicated in 6 regions spanning from the Mediterranean to the boreal biomes. Species richness and functional evenness of both bat and bird communities were affected by the interactions between latitude and forest composition and structure. Bat and bird species richness increased with broadleaved tree cover in temperate and especially in boreal regions but not in the Mediterranean where they increased with conifer abundance. Bat species richness was lower in forests with smaller trees and denser understorey only in northern regions. Bird species richness was not affected by forest structure. Bird functional evenness increased in younger and denser forests. Bat functional evenness was also influenced by interactions between latitude and understorey structure, increasing in temperate forests but decreasing in the Mediterranean. Covariation between bat and bird abundances also shifted across Europe, from negative in southern forests to positive in northern forests. Our results suggest that community assembly processes in bats and birds of European forests are predominantly driven by abundance and accessibility of feeding resources, i.e., insect prey, and their changes across both forest types and latitudes.

  6. Genetic diversity, temporal dynamics, and host specificity in blood parasites of passerines in north China.

    Science.gov (United States)

    Huang, Xi; Dong, Lu; Zhang, Chenglin; Zhang, Yanyun

    2015-12-01

    Avian blood parasites have been preliminarily studied in East Asia, but no data are available from long-term monitoring. The aim of this study was to evaluate the prevalence, genetic diversity, and temporal dynamics of Plasmodium, Haemoproteus, and Leucocytozoon in two passerine communities (one forest and one urban) in north China from 2008 to 2013, as well as the association between infected lineages and host specificities. Out of 633 birds from 40 species, 157 individuals (24.8 %) were infected; overall prevalence was 26.7 % and 16.8 % in two sites, respectively. The dominant avian blood parasite genus in the forest park changed yearly between Plasmodium and Haemoproteus, while the Leucocytozoon maintained a low infection level. Forty-four haplotypes were identified by sequencing a 432-bp fragment of the cytochrome b (cyt b) gene; more than 70 % were novel (six Plasmodium lineages, 16 Haemoproteus lineages, and nine Leucocytozoon lineages). Based on our data gathered over consecutive years, we found that the highly observed lineages of Haemoproteus showed higher host diversities than those of Plasmodium, and the most infected lineage EMEL01 (100 % identity with SGS1) take on the highest host diversity but low temporal diversity of the two genera, implying that this lineage infected a great diversity of species in certain years, but maintained a lower infection level or even disappeared in other years. The results suggest that genetic diversity of avian blood parasites in East Asia is high and provides scope for further research. In addition, compared with overall analysis, yearly prevalence monitoring is important in uncovering the temporal dynamic and host specificity variations over time.

  7. Genetic diversity of Metarhizium anisopliae var. anisopliae in southwestern British Columbia.

    Science.gov (United States)

    Inglis, G Douglas; Duke, Grant M; Goettel, Mark S; Kabaluk, J Todd

    2008-05-01

    The abundance and genetic diversity of the entomopathogenic fungus, Metarhizium anisopliae var. anisopliae, in southwestern British Columbia (BC) and southern Alberta was examined. The fungus was found to be widespread in soil throughout southwestern BC, and was recovered from 56% of 85 sample sites. In contrast to southwestern BC, no M. anisopliae isolates were recovered in southern Alberta. An automated fluorescent amplified fragment length polymorphism (AFLP) method was used to examine genetic diversity. In excess of 200 isolates were characterized. The method identified 211 polymorphic amplicons, ranging in size from approximately 92 to 400 base pairs, and it was found to be reproducible with a resolution limit of 86.2% similarity. The AFLP method distinguished Metarhizium from other entomopathogenic fungal genera, and demonstrated considerable genetic diversity (25 genotypes) among the reference strains of M. anisopliae isolates examined (i.e. recovered from various substrates and geographical locations). Although 13 genotypes of M. anisopliae var. anisopliae were recovered from southwestern BC soils, the vast majority of isolates (91%) belonged to one of two closely-related genotypes. Furthermore, these two genotypes predominated in urban, agricultural and forest soils. The reasons for the limited diversity of M. anisopliae var. anisopliae in southwestern BC are uncertain. However, findings of this study are consistent with island biogeography theory, and have significant implications for the development of this fungus for microbial control of pest insects.

  8. Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae).

    Science.gov (United States)

    Men, Qiulei; Xue, Guoxi; Mu, Dan; Hu, Qingling; Huang, Minyi

    2017-01-01

    Dendrolimus kikuchii Matsumura, 1927 is a serious forest pest causing great damage to coniferous trees in China. Despite its economic importance, the population genetics of this pest are poorly known. We used three mitochondrial genes (COI, COII and Cytb) to investigate the genetic diversity and genetic differentiation of 15 populations collected from the main distribution regions of D. kikuchii in China. Populations show high haplotype and nucleotide diversity. Haplotype network and phylogenetic analysis divides the populations into three major clades, the central and southeastern China (CC+SEC) clade, the eastern China (EC) clade, and the southwestern China (SWC) clade. Populations collected from adjacent localities share the same clade, which is consistent with the strong relationship of isolation by distance (r = 0.74824, P = 0.00001). AMOVA analysis indicated that the major portion of this molecular genetic variation is found among the three groups of CC+SEC, EC and SWC (61.26%). Of 105 pairwise FST comparisons, 93 show high genetic differentiation. Populations of Puer (PE), Yangshuo (YS) and Leishan (LS) are separated from other populations by a larger genetic distance. Distributions of pairwise differences obtained with single and combined gene data from the overall populations are multimodal, suggesting these populations had no prior population expansion in southern China. The nonsignificant neutral test on the basis of Tajima' D and Fu's Fs, and the lack of a star-shaped haplotype network together with the multiple haplotypes support this hypothesis. Pleistocene climatic fluctuations, combined with the host specificity to Pinus species, made these regions of south China into a refuge for D. kikuchii. The high level of population genetic structuring is related to their weak flight capacity, their variations of life history and the geographic distance among populations.

  9. GENETIC DIVERSITY OF THE WILD AND REARED PSEUDOSCIAENA CROCEA

    Institute of Scientific and Technical Information of China (English)

    王军; 苏永全; 全成干; 丁少雄; 张纹

    2001-01-01

    The genetic diversity of both wild and reared Pseudosciaena crocea (Richardson) col-lected from Guan-Jing-Yang in Ningde, China in May 1999 was investigated by random amplified poly-morphic DNA (RAPD) in the present study. The polymorphism and mean difference of the wild popula-tion as revealed by RAPD were 18.9% and 0.0960 respectively, and those of the reared stocks were rel-atively lower, with 16.7% in polymorphism and 0.0747 in mean difference. The genetic distance be-tween the two stocks was 0.0041. From the comprehensive investigation, the main reasons for the loss of genetic diversity were probably overilshing, small number of parents as broodstocks and the debatable arti-ficial ranching. Results from this study also showed that the large yellow croaker populations distributed along Fujian coastal waters including Guan-Jing-Yang still potentially wide genetic variability. It is sug-gested that genetic management and prevention should be scientifically conducted in order to maintain and improve the genetic diversity of the P. crocea population.

  10. Genetic diversity and population structure of cucumber (Cucumis sativus L..

    Directory of Open Access Journals (Sweden)

    Jing Lv

    Full Text Available Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

  11. 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.

  12. GENETIC DIVERSITY OF THE WILD AND REARED PSEUDOSCIAENA CROCEA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genetic diversity of both wild and reared Pseudosciaena crocea (Richardson) collected from Guan-Jing-Yang in Ningde, China in May 1999 was investigated by random amplified polymorphic DNA (RAPD) in the present study. The polymorphism and mean difference of the wild population as revealed by RAPD were 18.9% and 0.0960 respectively, and those of the reared stocks were relatively lower, with 16.7% in polymorphism and 0.0747 in mean difference. The genetic distance between the two stocks was 0.0041. From the comprehensive investigation, the main reasons for the loss of genetic diversity were probably overfishing, small number of parents as broodstocks and the debatable artificial ranching. Results from this study also showed that the large yellow croaker populations distributed along Fujian coastal waters including Guan-Jing-Yang still potentially wide genetic variability. It is suggested that genetic management and prevention should be scientifically conducted in order to maintain and improve the genetic diversity of the P. crocea population.

  13. Effect of fragmentation on the natural genetic diversity of Theobroma speciosum Willd. ex Spreng. populations.

    Science.gov (United States)

    Varella, T L; Rossi, A A B; Dardengo, J F E; Silveira, G F; Souza, M D A; Carvalho, M L S

    2016-11-21

    Forest fragmentation reduces the effective size of natural populations, isolates individuals in the landscape, and, consequently, changes species' mating systems by increasing the degree of relatedness between individuals and inbreeding. Investigating the impact of habitat degradation on forest fragments helps to assess the genetic and ecological consequences of these changes, and allows the development of effective and sustainable conservation strategies to manage the genetic resources of species living in degraded landscapes. The aim of the present study was to assess the genetic diversity of fragmented Theobroma speciosum populations using microsatellite markers. Three urban forest fragments were selected in the municipality of Alta Floresta, Mato Grosso State, Brazil, namely C/E park, J park, and Zoo Botanical park. Seventy-five individuals (25 in each fragment) were sampled by collecting their leaves for genomic DNA extraction. Polymerase chain reaction amplifications were performed using nine polymorphic simple sequence repeat primers, which amplified 84 alleles. The mean expected heterozygosity was 0.970, and it was always higher than the observed heterozygosity. Analysis of molecular variance revealed that most variability occurred within populations (64%) rather than between them (36%). The Structure software and an unweighted pair group method with arithmetic mean dendrogram revealed three distinct groups, showing that individuals were allocated to their correct populations. Genotype number 3 from C/E park, number 45 from J park, and number 51 from Zoo Botanical park could be used as stock plants in breeding programs, because they were the most dissimilar within the populations studied. The high genetic diversity levels detected in all three populations studied emphasize the importance of protecting this species in its natural habitat.

  14. Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

    Institute of Scientific and Technical Information of China (English)

    LU Yun-feng; LI Hong-wei; WU Ke-liang; WU Chang-xin

    2013-01-01

    Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity

  15. Genetic diversity of natural Hepatacodium miconioides populations in Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    LI Junmin; JIN Zexin

    2006-01-01

    Hepatacodium miconioides is the Class Ⅱ protected plant species in China.This paper studies the genetic diversity and differentiation of its nine natural populations in Zhejiang Province by using random amplified polymorphic DNA (RAPD) technique.Twelve random primers were selected in the amplification,and 164 repetitive loci were produced.The percentage of polymorphic loci in each H.miconioides population ranged from 14.60% to 27.44%,with an average of 20.73%.Among the test populations,Kuochangshan had the highest percentage of polymorphic loci,Simingshan took the second place,and Guanyinping had the lowest percentage.As estimated by Shannon index,the genetic diversity within H.miconioides populations accounted for 27.28% of the total genetic diversity,while that among H.miconioides populations accounted for 72.72%.The genetic differentiation among H.miconioides populations as estimated by Nei index was 0.715,7.This figure was generally consistent with that estimated by Shannon index,i.e.,the genetic differentiation among populations was relatively high,but that within populations was relatively low.The gene flow among H.miconioides populations was relatively low (0.198,7),and the genetic similarity ranged from 0.655,7 to 0.811,9,with an average of 0.730,6.The highest genetic distance among populations was 0.422,9,while the lowest was 0.208,3.All the results showed that there was a distinct genetic differentiation among H.miconioides populations.The genetic distance matrix of nine test populations was calculated using this method,and the clustering analysis was made using the unweighted pair group method with arithmetic mean (UPGMA).The cluster analysis suggested that the ninepopulations of H.miconioides in Zhejiang Province could be divided into two groups,the eastern Zhejiang group and the western Zhejiang group.

  16. Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

    Science.gov (United States)

    Edwards, F A; Edwards, D P; Larsen, T H; Hsu, W W; Benedick, S; Chung, A; Vun Khen, C; Wilcove, D S; Hamer, K C

    2014-01-01

    Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation. PMID:25821399

  17. Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

    Science.gov (United States)

    Edwards, F A; Edwards, D P; Larsen, T H; Hsu, W W; Benedick, S; Chung, A; Vun Khen, C; Wilcove, D S; Hamer, K C

    2014-04-01

    Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation.

  18. Gene diversity and genetic variation in lung flukes (genus Paragonimus).

    Science.gov (United States)

    Blair, David; Nawa, Yukifumi; Mitreva, Makedonka; Doanh, Pham Ngoc

    2016-01-01

    Paragonimiasis caused by lung flukes (genus Paragonimus) is a neglected disease occurring in Asia, Africa and the Americas. The genus is species-rich, ancient and widespread. Genetic diversity is likely to be considerable, but investigation of this remains confined to a few populations of a few species. In recent years, studies of genetic diversity have moved from isoenzyme analysis to molecular phylogenetic analysis based on selected DNA sequences. The former offered better resolution of questions relating to allelic diversity and gene flow, whereas the latter is more suitable for questions relating to molecular taxonomy and phylogeny. A picture is emerging of a highly diverse taxon of parasites, with the greatest diversity found in eastern and southern Asia where ongoing speciation might be indicated by the presence of several species complexes. Diversity of lung flukes in Africa and the Americas is very poorly sampled. Functional molecules that might be of value for immunodiagnosis, or as targets for medical intervention, are of great interest. Characterisation of these from Paragonimus species has been ongoing for a number of years. However, the imminent release of genomic and transcriptomic data for several species of Paragonimus will dramatically increase the rate of discovery of such molecules, and illuminate their diversity within and between species.

  19. Sequence variation and genetic diversity in the giant panda

    Institute of Scientific and Technical Information of China (English)

    张亚平; Oliver A.Ryder; 范志勇; 张和明; 何廷美; 何光昕; 张安居; 费立松; 钟顺隆; 陈红; 张成林; 杨明海; 朱飞兵; 彭真信; 普天春; 陈玉村; 姚敏达; 郭伟

    1997-01-01

    About 336-444 bp mitochondrial D-loop region and tRNA gene were sequenced for 40 individuals of the giant panda which were collected from Mabian, Meigu, Yuexi, Baoxing, Pingwu, Qingchuan, Nanping and Baishuijiang, respectively. 9 haplotypes were found in 21 founders. The results showed that the giant panda has low genetic variations, and that there is no notable genetic isolation among geographical populations. The ancestor of the living giant panda population perhaps appeared in the late Pleistocene, and unfortunately, might have suffered bottle-neck attacks. Afterwards, its genetic diversity seemed to recover to some extent.

  20. Soybean parent selection based on genetic diversity

    Directory of Open Access Journals (Sweden)

    Valéria Carpentieri-Pípolo

    2000-01-01

    Full Text Available Thirty-four soybean lines were assessed for twelve traits. The genetic distances were estimates using multivariate techniques, to identify parents to be included in breeding programs for hybridization. Grouping by the Tocher method, from generalized Mahalanobis distances, divided the 34 lines into four groups. The most important agronomic traits, weight of seeds per plot, plant height, height of first pod and days to maturity were considered when recommending for crossing. The following crosses were recommended based on the genetic divergence and the key agronomic traits: lines 23, 10, 2, 27 and 25 (group I with genotype 6 (group II and genotype 16 (group III. Thus only ten crosses would be made, representing only 2% of the total crosses which could be made in the partial diallel among the 34 lines assessed, which would allow up to 561 combinations.Trinta e quatro linhagens de soja foram avaliadas para doze características. As distâncias genéticas foram estimadas utilizando técnicas multivariadas com objetivo de identificar parentais a serem incluidos em um programa de melhoramento envolvendo hibridação. O agrupamento pelo método de Tocher, a partir das distâncias generalizadas de Mahalanobis, dividiu as 34 linhagens em 4 grupos. As caracterísiticas agronômicas mais importantes, peso de sementes por parcela, altura de planta, altura da primeira vagem e dias para maturação foram consideradas para a recomendação dos cruzamentos. Os seguintes cruzamentos foram recomendados baseado na divergência genética e nas características agronômicas chave: linhagens 23, 10, 2, 27 e 25 (grupo I com genótipo 6 (grupoII e com o genótipo 16 (grupo III. Portanto somente 10 cruzamentos poderiam ser realizados representando somente 2% do total de cruzamentos qu poderiam ser realizados em um dialelo parcial entre as 34 linhagens avaliadas as quais admitiriam até 561 combinações.

  1. Population structure and genetic diversity in natural populations of Theobroma speciosum Willd. Ex Spreng (Malvaceae).

    Science.gov (United States)

    Giustina, L D; Luz, L N; Vieira, F S; Rossi, F S; Soares-Lopes, C R A; Pereira, T N S; Rossi, A A B

    2014-02-14

    The genus Theobroma found in the Amazon region is composed of 22 species, including Theobroma speciosum, better known as cacauí. These species are constantly threatened by forest fragmentation caused by human activities and require conservation strategies and management aimed at preserving them in their natural environments. The main objective of this study was to analyze the population structure and genetic diversity within and between natural populations of T. speciosum by using ISSR molecular markers to understand the population structure of the species. Four natural populations belonging to the Amazon rainforest (BAC, CRO, FLA, and PNA), located in the State of Mato Grosso, were selected. Amplification reactions were performed using 15 ISSR primers. A total of 101 loci were found, of which 54.46% were polymorphic at the species level. The BAC population showed higher genetic diversity (H=0.095 and I=0.144) and higher percentage of polymorphism (28.71%). The populations showed an FST value of 0.604, indicating marked genetic differentiation. The highest genetic variation was found between populations. Gene flow was low between populations, indicating genetic isolation between populations.

  2. Landscape genetics, adaptive diversity and population structure in Phaseolus vulgaris.

    Science.gov (United States)

    Rodriguez, Monica; Rau, Domenico; Bitocchi, Elena; Bellucci, Elisa; Biagetti, Eleonora; Carboni, Andrea; Gepts, Paul; Nanni, Laura; Papa, Roberto; Attene, Giovanna

    2016-03-01

    Here we studied the organization of genetic variation of the common bean (Phaseolus vulgaris) in its centres of domestication. We used 131 single nucleotide polymorphisms to investigate 417 wild common bean accessions and a representative sample of 160 domesticated genotypes, including Mesoamerican and Andean genotypes, for a total of 577 accessions. By analysing the genetic spatial patterns of the wild common bean, we documented the existence of several genetic groups and the occurrence of variable degrees of diversity in Mesoamerica and the Andes. Moreover, using a landscape genetics approach, we demonstrated that both demographic processes and selection for adaptation were responsible for the observed genetic structure. We showed that the study of correlations between markers and ecological variables at a continental scale can help in identifying local adaptation genes. We also located putative areas of common bean domestication in Mesoamerica, in the Oaxaca Valley, and the Andes, in southern Bolivia-northern Argentina. These observations are of paramount importance for the conservation and exploitation of the genetic diversity preserved within this species and other plant genetic resources.

  3. Assessment of genetic diversity in Cattleya intermedia Lindl. (Orchidaceae

    Directory of Open Access Journals (Sweden)

    Nelson Barbosa Machado Neto

    2011-10-01

    Full Text Available Orchids are valuable pot plants and Cattleya intermedia is a promising species underused in breeding programs. Recently, breeding work with this species produced superior plants that are believed to be not the true species owing to the morphological differences from wild plants. The aim of this study was to estimate the level of genetic diversity and interrelationships between wild and bred Cattleya intermedia collected at three different Brazilian states and from commercial breeders with RAPD markers. A total of 65 polymorphic bands were used to generate a genetic distance matrix. No specific groupings were revealed by the cluster analysis as bred materials were not different from wild plants. The genetic differentiation (F ST = 0.01626 was very low indicating a high gene flow in C. intermedia due to artificial crosses and a high differentiation between populations. The genetic variability available within this species is high enough to allow genetic progress in flower shape and size.

  4. Genetic diversity in the Paramecium aurelia species complex.

    Science.gov (United States)

    Catania, Francesco; Wurmser, François; Potekhin, Alexey A; Przybos, Ewa; Lynch, Michael

    2009-02-01

    Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.

  5. Genetic diversity in diploid vs. tetraploid Rorippa amphibia (Brassicaceae)

    NARCIS (Netherlands)

    Luttikhuizen, P.C.; Stift, M.; Kuperus, P.; van Tienderen, P.H.

    2007-01-01

    The frequency of polyploidy increases with latitude in the Northern Hemisphere, especially in deglaciated, recently colonized areas. The cause or causes of this pattern are largely unknown, but a greater genetic diversity of individual polyploid plants due to a doubled genome and/or a hybrid origin

  6. Genetic diversity of Ascaris in southwestern Uganda

    DEFF Research Database (Denmark)

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia

    2012-01-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and M...

  7. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    This study aimed to assess the morphological variation, genetic diversity and ... questionnaire was used in recording both qualitative (coat color, eye color, horn ... these goat breeds have not yet undergone an organized breeding program. ... The Syrian goat populations had observed and expected heterozygosity values ...

  8. Ortholog identification in genera of high genetic diversity and evolution

    DEFF Research Database (Denmark)

    Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Frisvad, Jens Christian

    In the era of high-throughput sequencing, comparative genomics is vastly used in the discovery of genetic diversity between species, but also in defining the core and pan genome of single species to whole genera. Current comparative approaches are implementing ortholog identification to establish...... genome annotations, gene or protein evolutions or defining functional features in individual species and groups....

  9. Assessing genetic diversity of perennial ryegrass (Lolium perenne L ...

    African Journals Online (AJOL)

    Yomi

    2011-12-21

    Dec 21, 2011 ... cult to quantify, comparison of variability of traits over geological ... Africa, Asia and America. A second objective was to compare genetic diversity between commercial cultivars ...... population size when local extinction and recolonization of ... grosvenorii), an economic species endemic to South China, as.

  10. genetic diversity and prevalence of antiretroviral drug resistance ...

    African Journals Online (AJOL)

    PROGMANAGER

    2013-04-24

    Apr 24, 2013 ... Human immunodeficiency virus type-1 (HIV-1) genetic ... enrolled for HIV care at the Jos University Teaching Hospital (JUTH) HIV Treatment Center between ... algorithm. ..... and RT sequences revealed distribution of HIV-1 subtype's diversity circulating .... resistance position 210W; which is a rare finding.

  11. Morphological and molecular genetic diversity of Syrian indigenous ...

    African Journals Online (AJOL)

    Tuoyo Aghomotsegin

    2016-05-04

    May 4, 2016 ... This study aimed to assess the morphological variation, genetic diversity and population ... goat breed was well differentiated and grouped into a separate cluster that suggests its evolutionary ... research and development centers in representative ... Phenotypic and molecular characterizations have been.

  12. Genetic diversity and differentiation of Pseudophoenix (Arecaceae) in Hispaniola

    Science.gov (United States)

    Technical Abstract Pseudophoenix ekmanii Burret, P. lediniana Read, and P. vinifera (Mart.) Becc. (Arecaceae) are endemic to Hispaniola. The more wide-ranging P. sargentii H.Wendl. ex Sarg. occurs on this island as well. The population genetic diversity and structure of Pseudophoenix was investigate...

  13. Genetic diversity as assessed by morphological and microsatellite ...

    African Journals Online (AJOL)

    lap

    2012-10-18

    Oct 18, 2012 ... combination of morphological and molecular markers increases the efficiency of diversity measured and the adzuki bean microsatellite markers are highly polymorphic and can be successfully used .... information about the magnitude of genetic variability. ... Two primers MB77 and CP37 were monomorphic.

  14. Genetic diversity among varieties and wild species accessions of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... Key words: Genetic diversity, SSR, Pisum, cluster analysis, assignment test. INTRODUCTION ... phological characters and (or) molecular techniques (Ellis et al., 1998; Hoey et ..... Associations among 57 wild Pisum accessions and 20 varieties were ..... repeats (SSRs) in cultivated Brassica species. Theor.

  15. Genetic diversity and population structure of begomoviruses infecting sweet potato

    Science.gov (United States)

    Begomoviruses infecting sweet potatoes (Ipomoea batatas) exhibit high genetic diversity, and approximately eight species including Sweet potato leaf curl virus (SPLCV) have been described from different regions around the world. In this study, the complete genomic sequences of 17 geographically dist...

  16. Assessment of genetic diversity of sweet potato in Puerto Rico

    Science.gov (United States)

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand ...

  17. Genetic diversity of Actinobacillus lignieresii isolates from different hosts

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

    2011-01-01

    Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprisin...

  18. Molecular Diversity and Genetic Structure of Durum Wheat Landraces

    Directory of Open Access Journals (Sweden)

    GULNAR SHIKHSEYIDOVA

    2015-06-01

    Full Text Available To determine the genetic diversity of durum wheat, 41 accessions from Morocco, Ethiopia, Turkey, Lebanon, Kazakhstan, China, and Mongolia were analyzed through Inter-Simple Sequence Repeats (ISSR molecular markers. Out of the used twenty primers, 15 primers that included a considerable polymorphism were selected for the analyses. Among the genotypes under study, 163 fragments (73.7% were polymorph. Several indexes were used to determine the most appropriate primers. While UBC812, UBC864, UBC840, and UBC808 primers were among those markers which produced the highest number of bands and polymorphic bands, they also dedicated the highest rate of polymorphic index content (PIC. These primers also possessed the highest amounts of effective multiplex ratio (EMR and marker index (MI. Therefore, these primers can be recommended for genetic evaluation of the durum wheat. The results of cluster analysis and principle component analysis indicated that the observed genetic diversity in wheat materials under study is geographically structured. The results also indicated that the genetic diversity index based on ISSR markers was higher for Turkey, Lebanon, Morocco, and Ethiopia accessions than for other countries. The high level of polymorphism in this collections durum wheat would agree with the suggestion that Fertile Crescent and parts of Africa are first possible diversity center of this crop.

  19. Genetic Diversity Of Plukenetia Volubilis L. Assessed By ISSR Markers*

    Directory of Open Access Journals (Sweden)

    Ocelák M.

    2015-12-01

    Full Text Available The diversity and genetic relationships in 173 sacha inchi samples were analyzed using ISSR markers. Thirty ISSR primers were used, only 8 showed variability in tested samples. ISSR fragments ranged from 200 to 2500 bp. The mean number of bands per primer was 12 and the average number of polymorphic bands per primer was 11. The lowest percentages of polymorphic bands (27%, gene diversity (0.103, and Shannon’s information index (0.15 were exhibited by the Santa Lucia population, which was also geographically most distant. This fact may be attributed to a very small size of this group. In contrast, the Dos de Mayo population exhibited the highest percentage of polymorphic bands (78%, and the Santa Cruz population the highest Nei’s gene diversity index (0.238 and Shannon’s information index (0.357. The obtained level of genetic variability was 36% among tested populations and 64% within populations. Although the diversity indices were low, a cluster analysis revealed 8 clusters containing mainly samples belonging to individual populations. Principal coordinate analysis clearly distinguished Chumbaquihui, Pucallpa, Dos de Mayo, and Aguas de Oro populations, the others were intermixed. The obtained results indicated the level of genetic diversity present in this location of Peru, although it is influenced by anthropological aspects and independent on the geographical distances.

  20. Polyphenols in whole rice grain: genetic diversity and health benefits.

    Science.gov (United States)

    Shao, Yafang; Bao, Jinsong

    2015-08-01

    Polyphenols, such as phenolic acid, anthocyanin and proanthocyanidins, have both nutraceutical properties and functional significance for human health. Identification of polyphenolic compounds and investigation of their genetic basis among diverse rice genotypes provides the basis for the improvement of the nutraceutical properties of whole rice grain. This review focuses on current information on the identification, genetic diversity, formation and distribution patterns of the phenolic acid, anthocyanin, and proanthocyanidins in whole rice grain. The genetic analysis of polyphenol content and antioxidant capacity allows the identification of several candidate genes or quantitative trait loci (QTL) responsible for polyphenol variation, which may be useful in improvement of these phytochemicals by breeding. Future challenges such as how to mitigate the effects of climate change while improving nutraceutical properties in whole grain, and how to use new technology to develop new rice high in nutraceutical properties are also presented. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers.

    Science.gov (United States)

    Sen, Sandeep; Skaria, Reby; Abdul Muneer, P M

    2010-09-01

    The genetic diversity of eight species of Piper (Piperaceae) viz., P. nigrum, P. longum, P. betle, P. chaba, P. argyrophyllum, P. trichostachyon, P. galeatum, and P. hymenophyllum from Kerala state, India were analyzed by Random amplified polymorphic DNA (RAPD). Out of 22 10-mer RAPD primers screened, 11 were selected for comparative analysis of different species of Piper. High genetic variations were found among different Piper species studied. Among the total of 149 RAPD fragments amplified, 12 bands (8.05%) were found monomorphic in eight species. The remaining 137 fragments were found polymorphic (91.95%). Species-specific bands were found in all eight species studied. The average gene diversity or heterozygosity (H) was 0.33 across all the species, genetic distances ranged from 0.21 to 0.69. The results of this study will facilitate germplasm identification, management, and conservation.

  2. Genetic diversity of arginine catabolic mobile element in Staphylococcus epidermidis.

    Directory of Open Access Journals (Sweden)

    Maria Miragaia

    Full Text Available BACKGROUND: The methicillin-resistant Staphylococcus aureus clone USA300 contains a novel mobile genetic element, arginine catabolic mobile element (ACME, that contributes to its enhanced capacity to grow and survive within the host. Although ACME appears to have been transferred into USA300 from S. epidermidis, the genetic diversity of ACME in the latter species remains poorly characterized. METHODOLOGY/PRINCIPAL FINDINGS: To assess the prevalence and genetic diversity of ACME, 127 geographically diverse S. epidermidis isolates representing 86 different multilocus sequence types (STs were characterized. ACME was found in 51% (65/127 of S. epidermidis isolates. The vast majority (57/65 of ACME-containing isolates belonged to the predominant S. epidermidis clonal complex CC2. ACME was often found in association with different allotypes of staphylococcal chromosome cassette mec (SCCmec which also encodes the recombinase function that facilities mobilization ACME from the S. epidermidis chromosome. Restriction fragment length polymorphism, PCR scanning and DNA sequencing allowed for identification of 39 distinct ACME genetic variants that differ from one another in gene content, thereby revealing a hitherto uncharacterized genetic diversity within ACME. All but one ACME variants were represented by a single S. epidermidis isolate; the singular variant, termed ACME-I.02, was found in 27 isolates, all of which belonged to the CC2 lineage. An evolutionary model constructed based on the eBURST algorithm revealed that ACME-I.02 was acquired at least on 15 different occasions by strains belonging to the CC2 lineage. CONCLUSIONS/SIGNIFICANCE: ACME-I.02 in diverse S. epidermidis isolates were nearly identical in sequence to the prototypical ACME found in USA300 MRSA clone, providing further evidence for the interspecies transfer of ACME from S. epidermidis into USA300.

  3. Managing forest ecosystems to conserve fungus diversity and sustain wild mushroom harvests.

    Science.gov (United States)

    D. Pilz; R. Molina

    1996-01-01

    Ecosystem management is the dominant paradigm for managing the forests of the Pacific Northwest. It integrates biological, ecological, geophysical, and silvicultural information to develop adaptive management practices that conserve biological diversity and maintain ecosystem functioning while meeting human needs for the sustainable production of forest products. Fungi...

  4. SUBMONTANE FOREST AT BANTIMURUNG BULUSARAUNG NATIONAL PARK: HOTSPOT OF BIRD DIVERSITY AND ITS MANAGEMENT CONSERVATION

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    Indra A.S.L.P. Putri

    2015-09-01

    Full Text Available Submontane forest is considered as one of the biodiversity hotspot.  Scientific information on bird diversity in this forest, however are lacking.  The aim of this research was to find out submontane forest bird diversity and its conservation management.  The research was carried out in three forests areas at Bantimurung Bulusaraung National Park submontane forest.  Point Count method was used to observe bird population. Data were analyzed using Shannon-Weiner diversity index, Pielou Evenness index, Simpson dominance index, Margalef species richness index, and Sorensen Similarity index. The significance different between the number of individual bird was tested using Kolmogorov-Smirnov test.  The result showed that submontane forest at Bantimurung Bulusaraung National Park is rich in bird diversity, bird endemic species and protected bird species.  There was a significant different on the number of individual bird at several human disturbance levels.  Based on these conditions, it is important to enhance understanding of the local people regarding zonation and develop cooperation with many stakeholders to increase the local community awareness concerning forest conservation. It is also necessary to ensure the sustainability of the National Park’s conservation program to maintain the submontane forest conservation.

  5. Macrofungal diversity in Colombian Amazon forests varies with regions and regimes of disturbance

    NARCIS (Netherlands)

    Lopez-Quintero, C.A.; Straatsma, G.; Franco-Molano, A.E.; Boekhout, T.

    2012-01-01

    Here we present the results of fungal biodiversity studies from some selected Colombian Amazon forests in relationship to plant biodiversity and successional stages after slash and burn agriculture. Macrofungal diversity was found to differ between forests occurring in two regions (Araracuara vs Ama

  6. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

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    Sascha van der Meer

    Full Text Available Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68, which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  7. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems.

    Science.gov (United States)

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.

  8. Thai pigs and cattle production, genetic diversity of livestock and strategies for preserving animal genetic resources

    Directory of Open Access Journals (Sweden)

    Kesinee Gatphayak

    2013-03-01

    Full Text Available This paper reviews the current situation of livestock production in Thailand, genetic diversity and evaluation, as well as management strategies for animal genetic resources focusing on pigs and cattle. Sustainable conservation of indigenous livestock as a genetic resource and vital components within the agricultural biodiversity domain is a great challenge as well as an asset for the future development of livestock production in Thailand.

  9. Genetic diversity and molecular genealogy of local silkworm varieties

    Directory of Open Access Journals (Sweden)

    Zhouhe Du

    2013-03-01

    Full Text Available In order to explore the genetic diversity and systematic differentiation pattern among silkworm varieties, aiming to guide hybridization breeding, we sequenced a total of 72 Bmamy2 gene fragments from local silkworm varieties. The analysis of nucleotide sequence diversity and systematic differentiation indicated that there was rich genovariation in the sequencing region of Bmamy2 gene, and the base mutation rate is 5.6–8.2%, the haplotype diversity is 0.8294, and the nucleotide diversity is 0.0236±0.00122, suggesting Bmamy2 being a better marking gene with rich nucleotide sequence diversity, based on which the genetic diversity among different local silkworm varieties can be identified. The same heredity population structure is proclaimed by several analysis methods that every clade consisting of varieties from different geosystems and ecological types, while the varieties from the same geosystem and ecotype belong to different clades in the phylogeny. There is no population structure pattern that different varieties claded together according to geosystem or ecotype. It can be speculated that the silkworm origins from mixture of kinds of several voltinism mulberry silkworm, Bombyx mandarina, while the domestication events took place in several regions, from which the domesticated mulberry silkworms are all devoting to the domesticated silkworm population of today.

  10. Extraordinary Genetic Diversity in a Wood Decay Mushroom

    Science.gov (United States)

    Baranova, Maria A.; Logacheva, Maria D.; Penin, Aleksey A.; Seplyarskiy, Vladimir B.; Safonova, Yana Y.; Naumenko, Sergey A.; Klepikova, Anna V.; Gerasimov, Evgeny S.; Bazykin, Georgii A.; James, Timothy Y.; Kondrashov, Alexey S.

    2015-01-01

    Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10−8 (95% CI: 1.1 × 10−8 to 4.1 × 10−8) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. PMID:26163667

  11. Diversity did not influence soil water use of tree clusters in a temperate mixed forest

    OpenAIRE

    Meißner, M; Köhler, M; D. Hölscher

    2013-01-01

    Compared to monocultures, diverse ecosystems are often expected to show more comprehensive resource use. However, with respect to diversity–soil-water-use relationships in forests, very little information is available. We analysed soil water uptake in 100 tree clusters differing in tree species diversity and species composition in the Hainich forest in central Germany. The clusters contained all possible combinations of five broadleaved tree species in one-, two- and t...

  12. Contributions of a global network of tree diversity experiments to sustainable forest plantations

    OpenAIRE

    Verheyen, Kris; Vanhellemont, Margot; Auge, Harald; Baeten, Lander; Baraloto, Christopher; Barsoum, Nadia; Bilodeau-Gauthier, Simon; Bruelheide, Helge; Castagneyrol, Bastien; Godbold, Douglas; Haase, Josephine; Hector, Andy; Jactel, Hervé; Koricheva, Julia; LOREAU, Michel

    2016-01-01

    The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and...

  13. Generalist birds promote tropical forest regeneration and increase plant diversity via rare-biased seed dispersal.

    Science.gov (United States)

    Carlo, Tomás A; Morales, Juan M

    2016-07-01

    Regenerated forests now compose over half of the world's tropical forest cover and are increasingly important as providers of ecosystem services, freshwater, and biodiversity conservation. Much of the value and functionality of regenerating forests depends on the plant diversity they contain. Tropical forest diversity is strongly shaped by mutualistic interactions between plants and fruit-eating animals (frugivores) that disperse seeds. Here we show how seed dispersal by birds can influence the speed and diversity of early successional forests in Puerto Rico. For two years, we monitored the monthly fruit production of bird-dispersed plants on a fragmented landscape, and measured seed dispersal activity of birds and plant establishment in experimental plots located in deforested areas. Two predominantly omnivorous bird species, the Northern Mockingbird (Mimus polyglottos) and the Gray Kingbird (Tyrannus dominicensis), proved critical for speeding up the establishment of woody plants and increasing the species richness and diversity of the seed rain in deforested areas. Seed dispersal by these generalists increased the odds for rare plant species to disperse and establish in experimental forest-regeneration plots. Results indicate that birds that mix fruit and insects in their diets and actively forage across open and forested habitats can play keystone roles in the regeneration of mutualistic plant-animal communities. Furthermore, our analyses reveal that rare-biased (antiapostatic) frugivory and seed dispersal is the mechanism responsible for increasing plant diversity in the early-regenerating community. © 2016 by the Ecological Society of America.

  14. Tree diversity in the tropical dry forest of Bannerghatta National Park in Eastern Ghats, Southern India

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    Gopalakrishna S. Puttakame

    2015-12-01

    Full Text Available Tree species inventories, particularly of poorly known dry deciduous forests, are needed to protect and restore forests in degraded landscapes. A study of forest stand structure, and species diversity and density of trees with girth at breast height (GBH ≥10 cm was conducted in four management zones of Bannerghatta National Park (BNP in the Eastern Ghats of Southern India. We identified 128 tree species belonging to 45 families in 7.9 hectares. However, 44 species were represented by ≤ 2 individuals. Mean diversity values per site for the dry forest of BNP were: tree composition (23.8 ±7.6, plant density (100.69 ± 40.02, species diversity (2.56 ± 0.44 and species richness (10.48 ± 4.05. Tree diversity was not significantly different (P>0.05 across the four management zones in the park. However, the number of tree species identified significantly (P<0.05 increased with increasing number of sampling sites, but majority of the species were captured. Similarly, there were significant variations (p<0.05 between tree diameter class distributions. Juveniles accounted for 87% of the tree population. The structure of the forest was not homogeneous, with sections ranging from poorly structured to highly stratified configurations. The study suggests that there was moderate tree diversity in the tropical dry thorn forest of Bannerghatta National Park, but the forest was relatively young.

  15. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

    Science.gov (United States)

    The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characte...

  16. Species composition, diversity and relative abundance of amphibians in forests and non-forest habitats on Langkawi Island, Peninsular Malaysia

    Science.gov (United States)

    Nur Johana, J.; Muzzneena, A. M.; Grismer, L. L.; Norhayati, A.

    2016-11-01

    Anurans on Langkawi Island, Peninsular Malaysia exhibit variation in their habits and forms, ranging from small (SVL 150 mm), and occupy a range of habitats, such as riverine forests, agricultural fields, peat swamps, and lowland and upland dipterocarp forests. These variations provide a platform to explore species diversity, distribution, abundance, microhabitat, and other ecological parameters to understand the distribution patterns and to facilitate conservation and management of sensitive or important species and areas. The objective of this study was to evaluate the diversity and distribution of anuran species in different types of habitat on Langkawi Island. Specimens were collected based on active sampling using the Visual Encounter Survey (VES) method. We surveyed anuran species inhabiting seven types of habitat, namely agriculture (AG), coastal (CL), forest (FT), pond (PD), mangrove (MG), riparian forest (RF) and river (RV). A total of 775 individuals were sampled from all localities, representing 23 species from 12 genera and included all six families of frogs in Malaysia. FT and RF showed high values of Shannon Index, H', 2.60 and 2.38, respectively, followed by the other types of habitat, CL (1.82), RV (1.71), MG (1.56), PD (1.54), and AG (1.53). AG had the highest abundance (156 individuals) compared to other habitat types. Based on Cluster Analysis by using Jaccard coefficient (UPGMA), two groups can be clearly seen and assigned as forested species group (FT and RF) and species associating with human activity (AG, CL, PD, MG and RV). Forest species group is more diverse compared to non-forest group. Nevertheless, non-forest species are found in abundance, highlighting the relevance of these disturbed habitats in supporting the amphibians.

  17. [The effect of forest exploitation on structure, diversity, and floristic composition of palmito-dominated Atlantic forests at Misiones, Argentina].

    Science.gov (United States)

    Chediack, Sandra E

    2008-06-01

    The effect of forest exploitation--timber and palmito (Euterpe edulis, Palmae) extraction--on structure, diversity, and floristic composition of forests known as palmitals of the Atlantic Forest of Argentina was analyzed. These palmitals are located in Misiones (54 degrees 13' W and 25 degrees 41' S). Three 1 ha permanent plots were established: two in the "intangible" zone of the Iguazu National Park (PNI), and another in an exploited forest site bordering the PNI. Three 0.2 ha non-permanent plots were also measured. One was located in the PNI reserve zone where illegal palmito extraction occurs. The other two were in logged forest. All trees and palmitos with DBH >10 cm were identified and DBH and height were measured. For each of the six sites, richness and diversity of tree species, floristic composition, number of endemic species, and density of harvestable tree species were estimated. The harvest of E. edulis increases density of other tree species, diminishing palmito density. Forest explotation (logging and palmito harvest) is accompanied by an increase in diversity and density of heliophilic species, which have greater timber value in the region. However, this explotation also diminishes the density of palmito, of endemic species which normally grow in low densities, and of species found on the IUCN Red List. Results suggest that forest structure may be managed for timber and palmito production. The "intangible" zone of the PNI has the greatest conservation value in the Atlantic Forest, since a greater number of endemisms and endangered species are found here.

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

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    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.

  19. Diversity, structure and regeneration of the seasonally dry tropical forest of Yucatán Península, Mexico.

    OpenAIRE

    Hernández-Ramírez, Angélica María; García-Méndez, Socorro

    2015-01-01

    Seasonally dry tropical forests are considered as the most endangered ecosystem in lowland tropics. The aim of this study was to characterize the floristic composition, richness, diversity, structure and regeneration of a seasonally dry tropical forest landscape constituted by mature forest, secondary forest and seasonally inundated forest located in the Northeastern part of the Yucatán Península, Mexico. We used the Gentry’s standard inventory plot methodology (0.1 ha per forest type in 2007...

  20. Genetic diversity of Hungarian Maize dwarf mosaic virus isolates.

    Science.gov (United States)

    Gell, Gyöngyvér; Balázs, Ervin; Petrik, Kathrin

    2010-04-01

    The genetic diversity of the coat-protein (CP) region and the untranslated C-terminal region (3'UTR) of Maize dwarf mosaic virus (MDMV) was analyzed to evaluate the variability between isolates (inter-isolate sequence diversity). The results of inter-isolate sequence diversity analysis showed that the diversity of the MDMV CP gene is fairly high (p-distance: up to 0.136). During sequence analysis, a 13 amino-acid residue insertion and an 8 amino-acid residue deletion were found within the N-terminal region of the CP gene. The phylogenetic analysis showed that-unlike other potyvirus species in this subgroup-the MDMV isolates could not be distinguished on the basis of their host plants or geographic origins.

  1. Genetic diversity in a germplasm bank of Oenocarpus mapora (Arecaceae).

    Science.gov (United States)

    Moura, E F; de Oliveira, M S P

    2012-11-26

    Oenocarpus mapora is an Amazonian palm species commonly used by native populations for food and in folk medicine. We measured genetic variability, using RAPD markers, of material kept in a germplasm bank composed of accessions sampled from the Brazilian Amazon. These included 74 individuals from 23 accessions sampled from 9 localities in three States of the Brazilian Amazon. Jaccard genetic similarities were calculated based on 137 polymorphic bands, amplified by 15 primers. Dendrograms constructed based on the genetic similarities among individuals and sample localities demonstrated genetic separation of Acre State from the States of Amazonas and Pará. Two models in three hierarchical levels were considered for AMOVA: one considering the grouping of sampling sites in each state, and the other considering sampling sites in each subgroup formed by the dendrograms. The first model showed no significant genetic variation among states. On the other hand, genetic variation among subgroups was significant. In this model, the within-sample-site genetic diversity was 47.15%, which is considered to be low, since O. mapora is allogamous. By means of Bayesian analysis, the sample sites were clustered into five groups, and their distribution was similar to what we found in the dendrograms based on genetic similarity.

  2. Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria.

    Science.gov (United States)

    Couce, Alejandro; Rodríguez-Rojas, Alexandro; Blázquez, Jesús

    2016-07-01

    Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population's capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution.

  3. Microbialite genetic diversity and composition relate to environmental variables.

    Science.gov (United States)

    Centeno, Carla M; Legendre, Pierre; Beltrán, Yislem; Alcántara-Hernández, Rocío J; Lidström, Ulrika E; Ashby, Matthew N; Falcón, Luisa I

    2012-12-01

    Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H' = 6-7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  4. 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,

  5. The influence of recombination on human genetic diversity.

    Directory of Open Access Journals (Sweden)

    Chris C A Spencer

    2006-09-01

    Full Text Available In humans, the rate of recombination, as measured on the megabase scale, is positively associated with the level of genetic variation, as measured at the genic scale. Despite considerable debate, it is not clear whether these factors are causally linked or, if they are, whether this is driven by the repeated action of adaptive evolution or molecular processes such as double-strand break formation and mismatch repair. We introduce three innovations to the analysis of recombination and diversity: fine-scale genetic maps estimated from genotype experiments that identify recombination hotspots at the kilobase scale, analysis of an entire human chromosome, and the use of wavelet techniques to identify correlations acting at different scales. We show that recombination influences genetic diversity only at the level of recombination hotspots. Hotspots are also associated with local increases in GC content and the relative frequency of GC-increasing mutations but have no effect on substitution rates. Broad-scale association between recombination and diversity is explained through covariance of both factors with base composition. To our knowledge, these results are the first evidence of a direct and local influence of recombination hotspots on genetic variation and the fate of individual mutations. However, that hotspots have no influence on substitution rates suggests that they are too ephemeral on an evolutionary time scale to have a strong influence on broader scale patterns of base composition and long-term molecular evolution.

  6. Plant diversity after rain-forest fires in Borneo

    NARCIS (Netherlands)

    Eichhorn, Karl August Otto

    2006-01-01

    In the last two decades El-Niño-induced fires have caused widespread destruction of forests in East Kalimantan. The 1997-98 fires were the most extensive yet. The post-fire situation was studied in detail by field assessments and high-resolution SAR-images. My results show that rain forests are bett

  7. Forest-people interfaces : understanding community forestry and biocultural diversity

    NARCIS (Netherlands)

    Arts, B.J.M.; Bommel, van S.; Ros-Tonen, M.A.F.; Verschoor, G.M.

    2012-01-01

    This book aims at both academics and professionals in the field of forest-people interfaces. It takes the reader on a journey through four major themes that have emerged since the initiation of 'social forestry' in the 1970s: non-timber forest products and agroforestry; community-based natural resou

  8. Forest-people interfaces: understanding community forestry and biocultural diversity

    NARCIS (Netherlands)

    B. Arts; S. van Bommel; M. Ros-Tonen; G. Verschoor

    2012-01-01

    This book aims at both academics and professionals in the field of forest-people interfaces. It takes the reader on a journey through four major themes that have emerged since the initiation of 'social forestry' in the 1970s: non-timber forest products and agroforestry; community-based natural resou

  9. Genetic diversity in some local chicken breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-04-01

    Full Text Available Genetic relationships among Veneto native breeds of chickens were studied on the basis of microsatellites polymorphisms. A total of 100 DNA samples from 2 local chicken breeds (45 Robusta Lionata and 43 Robusta Maculata and a commercial broiler line (12 Golden Comet were analyzed using 19 microsatellite markers. The average number of alleles per locus was 4.05 and the expected heterozigosity resulted lower for the local breeds than the broiler line. The Robusta Lionata breed and the broiler line showed a significant deficit and excess of heterozygotes, respectively, deviating from Hardy-Weinberg equilibrium. Nei’s standard genetic distances corrected for bias due to sampling of individuals (Da, based on allele frequencies, were calculated among breeds. The local breeds resulted very similar confirming the same genetic origin. The results suggested that microsatellite markers are a useful tool for studying the genetic diversity among local chicken breeds.

  10. Genetic diversity affects colony survivorship in commercial honey bee colonies

    Science.gov (United States)

    Tarpy, David R.; vanEngelsdorp, Dennis; Pettis, Jeffrey S.

    2013-08-01

    Honey bee ( Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency ( m e ) of this population of honey bee queens to be 13.6 ± 6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ≤ 7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e > 7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated.

  11. Genetic diversity of symbiotic Paraburkholderia species isolated from nodules of Mimosa pudica (L.) and Phaseolus vulgaris (L.) grown in soils of the Brazilian Atlantic Forest (Mata Atlântica).

    Science.gov (United States)

    Dall'Agnol, Rebeca Fuzinatto; Bournaud, Caroline; de Faria, Sérgio Miana; Béna, Gilles; Moulin, Lionel; Hungria, Mariangela

    2017-04-01

    Some species of the genus Paraburkholderia that are able to nodulate and fix nitrogen in symbiosis with legumes are called β-rhizobia and represent a group of ecological and biotechnological importance. We used Mimosa pudica and Phaseolus vulgaris to trap 427 rhizobial isolates from rhizospheric soil of Mimoseae trees in the Brazilian Atlantic Forest. Eighty-four representative strains were selected according to the 16S rRNA haplotypes and taxonomically characterized using a concatenated 16S rRNA-recA phylogeny. Most strains were assembled in the genus Paraburkholderia, including Paraburkholderia sabiae and Pa. nodosa. Mesorhizobium (α-rhizobia) and Cupriavidus (β-rhizobia) were also isolated, but in smaller proportions. Multilocus sequence analysis and BOX-PCR analyses indicated that six clusters of Paraburkholderia represent potential new species. In the phylogenetic analysis of the nodC gene, the majority of the strains were positioned in the same groups as in the 16S rRNA-recA tree, indicative of stability and vertical inheritance, but we also identified horizontal transfer of nodC in Pa. sabiae. All α- and β-rhizobial species were trapped by both legumes, although preferences of the host plants for specific rhizobial species have been observed. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem.

    Science.gov (United States)

    Zytynska, Sharon E; Fay, Michael F; Penney, David; Preziosi, Richard F

    2011-05-12

    Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals.

  13. Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

    Directory of Open Access Journals (Sweden)

    Bráulio A Santos

    Full Text Available Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (<80 ha forest fragments. This was attributed to a reduction of 11% in the average phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

  14. 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.

  15. GENETIC DIVERSITY AND THE ORIGINS OF CULTURAL FRAGMENTATION

    Science.gov (United States)

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

    Despite the importance attributed to the effects of diversity on the stability and prosperity of nations, the origins of the uneven distribution of ethnic and cultural fragmentation across countries have been underexplored. Building on the role of deeply-rooted biogeographical forces in comparative development, this research empirically demonstrates that genetic diversity, predominantly determined during the prehistoric “out of Africa” migration of humans, is an underlying cause of various existing manifestations of ethnolinguistic heterogeneity. Further exploration of this uncharted territory may revolutionize the understanding of the effects of deeply-rooted factors on economic development and the composition of human capital across the globe. PMID:25506084

  16. Effects of forests, roads and mistletoe on bird diversity in monoculture rubber plantations

    Science.gov (United States)

    Sreekar, Rachakonda; Huang, Guohualing; Yasuda, Mika; Quan, Rui-Chang; Goodale, Eben; Corlett, Richard T.; Tomlinson, Kyle W.

    2016-02-01

    Rising global demand for natural rubber is expanding monoculture rubber (Hevea brasilensis) at the expense of natural forests in the Old World tropics. Conversion of forests into rubber plantations has a devastating impact on biodiversity and we have yet to identify management strategies that can mitigate this. We determined the life-history traits that best predict bird species occurrence in rubber plantations in SW China and investigated the effects of surrounding forest cover and distance to roads on bird diversity. Mistletoes provide nectar and fruit resources in rubber so we examined mistletoe densities and the relationship with forest cover and rubber tree diameter. In rubber plantations, we recorded less than half of all bird species extant in the surrounding area. Birds with wider habitat breadths and low conservation value had a higher probability of occurrence. Species richness and diversity increased logarithmically with surrounding forest cover, but roads had little effect. Mistletoe density increased exponentially with rubber tree diameters, but was unrelated to forest cover. To maximize bird diversity in rubber-dominated landscapes it is therefore necessary to preserve as much forest as possible, construct roads through plantations and not forest, and retain some large rubber trees with mistletoes during crop rotations.

  17. Effects of Previous Land-Use on Plant Species Composition and Diversity in Mediterranean Forests.

    Science.gov (United States)

    Kouba, Yacine; Martínez-García, Felipe; de Frutos, Ángel; Alados, Concepción L

    2015-01-01

    At some point in their history, most forests in the Mediterranean Basin have been subjected to intensive management or converted to agriculture land. Knowing how forest plant communities recovered after the abandonment of forest-management or agricultural practices (including livestock grazing) provides a basis for investigating how previous land management have affected plant species diversity and composition in forest ecosystems. Our study investigated the consequences of historical "land management" practices on present-day Mediterranean forests by comparing species assemblages and the diversity of (i) all plant species and (ii) each ecological group defined by species' habitat preferences and successional status (i.e., early-, mid-, and late-successional species). We compared forest stands that differed both in land-use history and in successional stage. In addition, we evaluated the value of those stands for biodiversity conservation. The study revealed significant compositional differentiation among stands that was due to among-stand variations in the diversity (namely, species richness and evenness) of early-, intermediate-, and late-successional species. Historical land management has led to an increase in compositional divergences among forest stands and the loss of late-successional forest species.

  18. Changes in ground beetle diversity and community composition in age structured forests (Coleoptera, Carabidae

    Directory of Open Access Journals (Sweden)

    Kathryn Riley

    2011-11-01

    Full Text Available We examined diversity, community composition, and wing-state of Carabidae as a function of forest age in Piedmont North Carolina. Carabidae were collected monthly from 396 pitfall traps (12×33 sites from March 2009 through February 2010, representing 5 forest age classes approximately 0, 10, 50, 85, and 150 years old. A total of 2,568 individuals, representing 30 genera and 63 species, were collected. Carabid species diversity, as estimated by six diversity indices, was significantly different between the oldest and youngest forest age classes for four of the six indices. Most carabid species were habitat generalists, occurring in all or most of the forest age classes. Carabid species composition varied across forest age classes. Seventeen carabid species were identified as potential candidates for ecological indicators of forest age. Non-metric multidimensional scaling (NMDS showed separation among forest age classes in terms of carabid beetle community composition. The proportion of individuals capable of flight decreased significantly with forest age.

  19. Genetic diversity and selection regulates evolution of infectious bronchitis virus.

    Science.gov (United States)

    Toro, Haroldo; van Santen, Vicky L; Jackwood, Mark W

    2012-09-01

    Conventional and molecular epidemiologic studies have confirmed the ability of infectious bronchitis virus (IBV) to rapidly evolve and successfully circumvent extensive vaccination programs implemented since the early 1950s. IBV evolution has often been explained as variation in gene frequencies as if evolution were driven by genetic drift alone. However, the mechanisms regulating the evolution of IBV include both the generation of genetic diversity and the selection process. IBV's generation of genetic diversity has been extensively investigated and ultimately involves mutations and recombination events occurring during viral replication. The relevance of the selection process has been further understood more recently by identifying genetic and phenotypic differences between IBV populations prior to, and during, replication in the natural host. Accumulating evidence suggests that multiple environmental forces within the host, including immune responses (or lack thereof) and affinity for cell receptors, as well as physical and biochemical conditions, are responsible for the selection process. Some scientists have used or adopted the related quasispecies frame to explain IBV evolution. The quasispecies frame, while providing a distinct explanation of the dynamics of populations in which mutation is a frequent event, exhibits relevant limitations which are discussed herein. Instead, it seems that IBV populations evolving by the generation of genetic variability and selection on replicons follow the evolutionary mechanisms originally proposed by Darwin. Understanding the mechanisms underlying the evolution of IBV is of basic relevance and, without doubt, essential to appropriately control and prevent the disease.

  20. Turtle carapace anomalies: the roles of genetic diversity and environment.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    Full Text Available BACKGROUND: Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. CONCLUSIONS/SIGNIFICANCE: Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations.

  1. Analysis of Structure and Diversity of the Kilengwe Forest in the Morogoro Region, Tanzania

    Directory of Open Access Journals (Sweden)

    David Sylvester Kacholi

    2014-01-01

    Full Text Available This study investigates the structure, species composition, and diversity of a section of the Kilengwe Forest in Tanzania. In order to accomplish the proposed objectives, 18 plots of 20 m × 20 m were randomly established in the forest and the number of tree species in each plot was identified and counted. The most important families and species were determined using importance value indices at the respective taxonomic levels. Diversity was measured using the Shannon-Wiener and Fisher alpha diversity indices. A total of 276 stems/ha representing 93 species/ha within 26 families were documented from 0.72 ha. Fabaceae and Julbernadia globiflora were the dominant family and species, respectively. Seventy-eight percent of the total species were rare. The average basal area of the forest was 7.1 m2/ha. The Shannon-Wiener index (4.02 and Fisher’s alpha diversity (35.5 indicated high species diversity within the forest. The species-area and species-abundance curves revealed an escalating trend implying that more sampling efforts could result in a higher number of species existing in the forest. The size class distribution displayed a reverse J-shaped pattern; however, the larger size classes DBH >50 cm were not represented. The study suggests the necessity for anthropogenic disturbance control as this is the major source of forest degradation in the studied area.

  2. Study on forest landscape diversity based on ArcGIS and GS +

    Science.gov (United States)

    Zhang, Yujuan; Qu, Jianguang; Liu, Dandan; Yang, Jinling; Li, Dan

    2015-12-01

    This paper analyses the forest landscape diversity of the study area with the help of ArcGIS10 and GS+ software. The forest landscape diversity and spatial interpolation and spatial differentiation are also carried out. The result shows that the maximum value of SHDI in 1997is 2.0463 and the minimum value is 0.2544 , which are 1.9722 and 0.2418 in the year of 2009. The advantage religion of SHDI mainly distributes in the middle of the study region , showing a band region from southwest to northeast . The forest landscape diversity and the space location have a moderate spatial correlation and a obvious structural under a forest level.

  3. Drought-adaptation potential in Fagus sylvatica: linking moisture availability with genetic diversity and dendrochronology.

    Directory of Open Access Journals (Sweden)

    Andrea R Pluess

    Full Text Available BACKGROUND: Microevolution is essential for species persistence especially under anticipated climate change scenarios. Species distribution projection models suggested that the dominant tree species of lowland forests in Switzerland, European beech (Fagus sylvatica L., might disappear from most areas due to expected longer dry periods. However, if genotypes at the moisture boundary of the species climatic envelope are adapted to lower moisture availability, they can serve as seed source for the continuation of beech forests under changing climates. METHODOLOGY/PRINCIPAL FINDINGS: With an AFLP genome scan approach, we studied neutral and potentially adaptive genetic variation in Fagus sylvatica in three regions containing a dry and a mesic site each (n(ind. = 241, n(markers = 517. We linked this dataset with dendrochronological growth measures and local moisture availabilities based on precipitation and soil characteristics. Genetic diversity decreased slightly at dry sites. Overall genetic differentiation was low (F(st = 0.028 and Bayesian cluster analysis grouped all populations together suggesting high (historical gene flow. The Bayesian outlier analyses indicated 13 markers with three markers differing between all dry and mesic sites and the others between the contrasting sites within individual regions. A total of 41 markers, including seven outlier loci, changed their frequency with local moisture availability. Tree height and median basal growth increments were reduced at dry sites, but marker presence/absence was not related to dendrochronological characteristics. CONCLUSION AND THEIR SIGNIFICANCE: The outlier alleles and the makers with changing frequencies in relation to moisture availability indicate microevolutionary processes occurring within short geographic distances. The general genetic similarity among sites suggests that 'preadaptive' genes can easily spread across the landscape. Yet, due to the long live span of

  4. Drought-adaptation potential in Fagus sylvatica: linking moisture availability with genetic diversity and dendrochronology.

    Science.gov (United States)

    Pluess, Andrea R; Weber, Pascale

    2012-01-01

    Microevolution is essential for species persistence especially under anticipated climate change scenarios. Species distribution projection models suggested that the dominant tree species of lowland forests in Switzerland, European beech (Fagus sylvatica L.), might disappear from most areas due to expected longer dry periods. However, if genotypes at the moisture boundary of the species climatic envelope are adapted to lower moisture availability, they can serve as seed source for the continuation of beech forests under changing climates. With an AFLP genome scan approach, we studied neutral and potentially adaptive genetic variation in Fagus sylvatica in three regions containing a dry and a mesic site each (n(ind.) = 241, n(markers) = 517). We linked this dataset with dendrochronological growth measures and local moisture availabilities based on precipitation and soil characteristics. Genetic diversity decreased slightly at dry sites. Overall genetic differentiation was low (F(st) = 0.028) and Bayesian cluster analysis grouped all populations together suggesting high (historical) gene flow. The Bayesian outlier analyses indicated 13 markers with three markers differing between all dry and mesic sites and the others between the contrasting sites within individual regions. A total of 41 markers, including seven outlier loci, changed their frequency with local moisture availability. Tree height and median basal growth increments were reduced at dry sites, but marker presence/absence was not related to dendrochronological characteristics. CONCLUSION AND THEIR SIGNIFICANCE: The outlier alleles and the makers with changing frequencies in relation to moisture availability indicate microevolutionary processes occurring within short geographic distances. The general genetic similarity among sites suggests that 'preadaptive' genes can easily spread across the landscape. Yet, due to the long live span of trees, fostering saplings originating from dry sites and

  5. Genetic effects of air pollution on forest tree species of the Carpathian Mountains

    Energy Technology Data Exchange (ETDEWEB)

    Longauer, Roman; Goemoery, Dusan; Paule, Ladislav; Blada, Ioan; Popescu, Flaviu; Mankovska, Blanka; Mueller-Starck, Gerhard; Schubert, Roland; Percy, Kevin; Szaro, Robert C.; Karnosky, David F

    2004-07-01

    The effects of air pollution on the genetic structure of Norway spruce, European silver fir and European beech were studied at four polluted sites in Slovakia, Romania and Czech Republic. In order to reduce potential effects of site heterogeneity on the health condition, pair-wise sampling of pollution-tolerant and sensitive trees was applied. Genotypes of sampled trees were determined at 21 isozyme gene loci of spruce, 18 loci of fir and 15 loci of beech. In comparison with Norway spruce, fewer genetic differences were revealed in beech and almost no differentiation between pollution-tolerant and sensitive trees was observed in fir. In adult stands of Norway spruce, sensitive trees exhibited higher genetic multiplicity and diversity. The decline of pollution-sensitive trees may result thus in a gradual genetic depletion of pollution-exposed populations of Norway spruce through the loss of less frequent alleles with potential adaptive significance to altered stressing regimes in the future. Comparison of the subsets of sensitive and tolerant Norway spruce individuals as determined by presence or absence of discolorations (''spruce yellowing'') revealed different heterozygosity at 3 out of 11 polymorphic loci. - Genetic effects of air pollution on main forest trees of the Carpathians are species- and site-specific.

  6. Effect of multi-temporal forest cover change trajectories on forest plant diversity

    Science.gov (United States)

    One of the principal tenets of landscape ecology is that forest loss and fragmentation negatively affects biodiversity. However, historical fluctuations in forest cover resulting from repeated cycles of deforestation and reforestation are likely important in influencing patterns ...

  7. Biological Diversity of Created Forested Wetlands in Comparison to Reference Forested Wetlands in the Bay Watershed

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Amphibians, reptiles, birds, and mammals were surveyed at six created forested wetlands in central Maryland and at six adjacent reference forested wetlands during...

  8. Serving culturally diverse visitors to forests in California: a resource guide

    Science.gov (United States)

    Nina S. Roberts; Deborah J. Chavez; Benjamin M. Lara; Emilyn A. Sheffield

    2009-01-01

    The national forests of California are experiencing an increase in new visitors yet, in some areas, a continued lack of ethnic diversity persists. In addition, changing demographics has led to a need for keeping up with trends while also being aware of constraints to visitor use. Knowing how to serve culturally diverse visitors in ways that are innovative and inclusive...

  9. Plant-animal interactions in two forest herbs along a tree and herb diversity gradient

    NARCIS (Netherlands)

    Vockenhuber, E.; Kabouw, P.; Tscharntke, T.; Scherber, C.

    2013-01-01

    Background: Plant diversity can influence numerous ecosystem processes, including plant–animal interactions, which, in turn, will affect plant growth and fitness. At present, little is known on how plant–animal interactions in forests respond to gradients in tree and herb-layer diversity. Aims: To q

  10. Arthropod Diversity and Functional Importance in Old-Growth Forests of North America

    Directory of Open Access Journals (Sweden)

    Timothy Schowalter

    2017-03-01

    Full Text Available Old-growth forests have become rare in North America but provide habitat for unique assemblages of species that often are rare in younger forests. Insects and related arthropods reach their highest diversity in old-growth forests because of their stable moderate temperature and relative humidity and the rich variety of resources represented by high plant species richness and structural complexity. Old-growth arthropod assemblages typically are distinct from those in younger, managed forests. Major subcommunities include the arboreal community that is composed of a rich assemblage of herbivores, fungivores, and their associated predators and parasitoids that function to regulate primary production and nutrient fluxes, the stem zone community that includes bark- and wood-boring species and their associated predators and parasitoids that initiate the decomposition of coarse woody debris, and the forest floor community composed of a variety of detritivores, fungivores, burrowers, and their associated predators and parasitoids that are instrumental in litter decomposition. Insect outbreaks are relatively rare in old-growth forests, where the diversity of resources and predators limit population growth. In turn, insects contribute to plant diversity and limit primary production of host plant species, thereby promoting development of old-growth forest characteristics. Arthropods also provide important functions in decomposition and nutrient cycling that may be lost in younger, managed forests with limited provision of coarse woody debris and accumulated litter. Protection of remnant old-growth forests within the forest matrix may be particularly valuable for maintaining the diversity of plant and arthropod predators that can minimize outbreaks, thereby contributing to resilience to changing environmental conditions.

  11. Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

    Directory of Open Access Journals (Sweden)

    Ermis Yanes Paz

    2012-01-01

    Full Text Available The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

  12. Bartonella Prevalence and Genetic Diversity in Small Mammals from Ethiopia

    DEFF Research Database (Denmark)

    Meheretu, Yonas; Leirs, Herwig E.l.; Welegerima, Kiros

    2013-01-01

    More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Barto......More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp...... of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals...

  13. Morphological and genetic diversity of symbiotic cyanobacteria from cycads.

    Science.gov (United States)

    Thajuddin, Nooruddin; Muralitharan, Gangatharan; Sundaramoorthy, Mariappan; Ramamoorthy, Rengasamy; Ramachandran, Srinivasan; Akbarsha, Mohamed Abdulkadar; Gunasekaran, Muthukumaran

    2010-06-01

    The morphological and genetic diversity of cyanobacteria associated with cycads was examined using PCR amplification techniques and 16S rRNA gene sequence analysis. Eighteen symbiotic cyanobacteria were isolated from different cycad species. One of the symbiotic isolates was a species of Calothrix, a genus not previously reported to form symbioses with Cycadaceae family, and the remainder were Nostoc spp. Axenic cyanobacterial strains were compared by DNA amplification using PCR with either short arbitrary primers or primers specific for the repetitive sequences. Based on fingerprint patterns and phenograms, it was revealed that cyanobacterial symbionts exhibit important genetic diversity among host plants, both within and between cycad populations. A phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that most of the symbiotic cyanobacterial isolates fell into well-separated clades.

  14. Isolation of genetically diverse Marburg viruses from Egyptian fruit bats.

    Science.gov (United States)

    Towner, Jonathan S; Amman, Brian R; Sealy, Tara K; Carroll, Serena A Reeder; Comer, James A; Kemp, Alan; Swanepoel, Robert; Paddock, Christopher D; Balinandi, Stephen; Khristova, Marina L; Formenty, Pierre B H; Albarino, Cesar G; Miller, David M; Reed, Zachary D; Kayiwa, John T; Mills, James N; Cannon, Deborah L; Greer, Patricia W; Byaruhanga, Emmanuel; Farnon, Eileen C; Atimnedi, Patrick; Okware, Samuel; Katongole-Mbidde, Edward; Downing, Robert; Tappero, Jordan W; Zaki, Sherif R; Ksiazek, Thomas G; Nichol, Stuart T; Rollin, Pierre E

    2009-07-01

    In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.

  15. Bartonella Prevalence and Genetic Diversity in Small Mammals from Ethiopia

    DEFF Research Database (Denmark)

    Meheretu, Yonas; Leirs, Herwig E.l.; Welegerima, Kiros;

    2013-01-01

    More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Barto......More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp...... of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals...

  16. Isolation of genetically diverse Marburg viruses from Egyptian fruit bats.

    Directory of Open Access Journals (Sweden)

    Jonathan S Towner

    2009-07-01

    Full Text Available In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus based on detection of Marburg virus RNA in 31/611 (5.1% bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.

  17. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

    Science.gov (United States)

    Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

    2016-05-01

    A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.

  18. A genomic scale map of genetic diversity in Trypanosoma cruzi

    Directory of Open Access Journals (Sweden)

    Ackermann Alejandro A

    2012-12-01

    Full Text Available Abstract Background Trypanosoma cruzi, the causal agent of Chagas Disease, affects more than 16 million people in Latin America. The clinical outcome of the disease results from a complex interplay between environmental factors and the genetic background of both the human host and the parasite. However, knowledge of the genetic diversity of the parasite, is currently limited to a number of highly studied loci. The availability of a number of genomes from different evolutionary lineages of T. cruzi provides an unprecedented opportunity to look at the genetic diversity of the parasite at a genomic scale. Results Using a bioinformatic strategy, we have clustered T. cruzi sequence data available in the public domain and obtained multiple sequence alignments in which one or two alleles from the reference CL-Brener were included. These data covers 4 major evolutionary lineages (DTUs: TcI, TcII, TcIII, and the hybrid TcVI. Using these set of alignments we have identified 288,957 high quality single nucleotide polymorphisms and 1,480 indels. In a reduced re-sequencing study we were able to validate ~ 97% of high-quality SNPs identified in 47 loci. Analysis of how these changes affect encoded protein products showed a 0.77 ratio of synonymous to non-synonymous changes in the T. cruzi genome. We observed 113 changes that introduce or remove a stop codon, some causing significant functional changes, and a number of tri-allelic and tetra-allelic SNPs that could be exploited in strain typing assays. Based on an analysis of the observed nucleotide diversity we show that the T. cruzi genome contains a core set of genes that are under apparent purifying selection. Interestingly, orthologs of known druggable targets show statistically significant lower nucleotide diversity values. Conclusions This study provides the first look at the genetic diversity of T. cruzi at a genomic scale. The analysis covers an estimated ~ 60% of the genetic diversity present in the

  19. Genetic diversity and maternal origin of Bangladeshi chicken.

    Science.gov (United States)

    Bhuiyan, M S A; Chen, Shanyuan; Faruque, S; Bhuiyan, A K F H; Beja-Pereira, Albano

    2013-06-01

    Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of

  20. Genetic and phenotypic diversity in breast tumor metastases.

    Science.gov (United States)

    Almendro, Vanessa; Kim, Hee Jung; Cheng, Yu-Kang; Gönen, Mithat; Itzkovitz, Shalev; Argani, Pedram; van Oudenaarden, Alexander; Sukumar, Saraswati; Michor, Franziska; Polyak, Kornelia

    2014-03-01

    Metastatic disease is the main cause of cancer-related mortality due to almost universal therapeutic resistance. Despite its high clinical relevance, our knowledge of how cancer cell populations change during metastatic progression is limited. Here, we investigated intratumor genetic and phenotypic heterogeneity during metastatic progression of breast cancer. We analyzed cellular genotypes and phenotypes at the single cell level by performing immunoFISH in intact tissue sections of distant metastatic tumors from rapid autopsy cases and from primary tumors and matched lymph node metastases collected before systemic therapy. We calculated the Shannon index of intratumor diversity in all cancer cells and within phenotypically distinct cell populations. We found that the extent of intratumor genetic diversity was similar regardless of the chromosomal region analyzed, implying that it may reflect an inherent property of the tumors. We observed that genetic diversity was highest in distant metastases and was generally concordant across lesions within the same patient, whereas treatment-naïve primary tumors and matched lymph node metastases were frequently genetically more divergent. In contrast, cellular phenotypes were more discordant between distant metastases than primary tumors and matched lymph node metastases. Diversity for 8q24 was consistently higher in HER2(+) tumors compared with other subtypes and in metastases of triple-negative tumors relative to primary sites. We conclude that our integrative method that couples ecologic models with experimental data in human tissue samples could be used for the improved prognostication of patients with cancer and for the design of more effective therapies for progressive disease.

  1. Assessment of genetic diversity of Xanthomonas oryzae pv. oryzae

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@Bacterial blight of rice, caused by Xanthomonas oryzae pv. Oryzae(Xoo. ), is one of the major rice diseases in China. Making clear the shift of genetic diversity of the pathogen will provide important information for rice breeding. Strains collected from 11 provinces located in Southern region of the Changjiang River in China were assessed by using inoculation method and IS-PCR(Insertion Sequence-Based Polymerase Chain Reaction) analysis.

  2. Limited Pollen Dispersal Contributes to Population Genetic Structure but Not Local Adaptation in Quercus oleoides Forests of Costa Rica.

    Directory of Open Access Journals (Sweden)

    Nicholas John Deacon

    Full Text Available Quercus oleoides Cham. and Schlect., tropical live oak, is a species of conservation importance in its southern range limit of northwestern Costa Rica. It occurs in high-density stands across a fragmented landscape spanning a contrasting elevation and precipitation gradient. We examined genetic diversity and spatial genetic structure in this geographically isolated and genetically distinct population. We characterized population genetic diversity at 11 nuclear microsatellite loci in 260 individuals from 13 sites. We monitored flowering time at 10 sites, and characterized the local environment in order to compare observed spatial genetic structure to hypotheses of isolation-by-distance and isolation-by-environment. Finally, we quantified pollen dispersal distances and tested for local adaptation through a reciprocal transplant experiment in order to experimentally address these hypotheses.High genetic diversity is maintained in the population and the genetic variation is significantly structured among sampled sites. We identified 5 distinct genetic clusters and average pollen dispersal predominately occurred over short distances. Differences among sites in flowering phenology and environmental factors, however, were not strictly associated with genetic differentiation. Growth and survival of upland and lowland progeny in their native and foreign environments was expected to exhibit evidence of local adaptation due to the more extreme dry season in the lowlands. Seedlings planted in the lowland garden experienced much higher mortality than seedlings in the upland garden, but we did not identify evidence for local adaptation.Overall, this study indicates that the Costa Rican Q. oleoides population has a rich population genetic history. Despite environmental heterogeneity and habitat fragmentation, isolation-by-distance and isolation-by-environment alone do not explain spatial genetic structure. These results add to studies of genetic structure by

  3. Genetic diversity and differentiation of Pinus sylvestris L. from the IUFRO 1982 provenance trial revealed by AFLP analysis

    Directory of Open Access Journals (Sweden)

    Androsiuk Piotr

    2015-01-01

    Full Text Available DNA markers have become effective tools in genetic diversity studies of forest trees. However, molecular marker analyses are associated with laborious and costly effort. One of the possibilities to overcome these constraints is to analyze bulked samples per population, rather than individual plants. We have used bulked DNA-based AFLP analysis to investigate genetic variations in Pinus sylvestris L. (Scots pine from the IUFRO 1982 provenance trial in Kórnik (western Poland. Four AFLP primer combinations yielded a total of 309 bands, of which 208 (67.31% were polymorphic. Thirty-six (11.65% unique alleles were deployed randomly among the populations. Estimated genetic diversity and differentiation was high, as expressed by He = 0.238 and I = 0.356, and by genetic distance values which ranged from 0.154 to 0.363. A geographic pattern of interpopulation differentiation was observed, pointing to the individual character of populations from northeastern Europe. In the light of available data, we discuss the influence of historical migration routes, gene flow and human activity on observed genetic diversity and differentiation of Scots pine in Europe. Our results indicate that the AFLP method applied to DNA templates extracted from bulked leaf samples provides an efficient approach to elucidate genetic diversity and relationships among Scots pine populations.

  4. Effects of Bamboo Fargesia murielae on Plant Diversity in Fir Forest on Mountain Shennongjia

    Institute of Scientific and Technical Information of China (English)

    Li Zhaohua; Manfred Denich; Thomas Borsch

    2004-01-01

    Simultaneous flowering caused a gregarious dieback of umbrella bamboo (Fargesia murielae) all over the world in 1993-2000. Mountain Shennongjia in Central China's Hubei Province is the only native home of umbrella bamboo, where it dominates the understorey of the farges fir (Abies fargesii) forest between 2 400 and 3 100 m, covering the ground for more than one century before a periodically flowering death. Data from 20 quadrats along a vegetation sequence revealed that the density, coverage, and height of umbrella bamboo negatively affected the species richness, diversity, and evenness of vascular plants in the forest. Local climax community of fir-bamboo was the poorest in species diversity, while the bamboo-free communities (i.e. shrubs and meadows) were bearing a higher species diversity. The simultaneous dieback of umbrella bamboo is an ecological release, which can periodically promote the plant diversity in the fir forest.

  5. Dry coniferous forest restoration and understory plant diversity: The importance of community heterogeneity and the scale of observation

    Science.gov (United States)

    Erich Kyle Dodson; David W. Peterson

    2010-01-01

    Maintaining understory plant species diversity is an important management goal as forest restoration and fuel reduction treatments are applied extensively to dry coniferous forests of western North America. However, understory diversity is a function of both local species richness (number of species in a sample unit) and community heterogeneity (beta diversity) at...

  6. Analysis of Genetic Diversity Among Sweetpotato Landraces in China

    Institute of Scientific and Technical Information of China (English)

    HE Xue-qin; LIU Qing-chang; WANG Yu-ping; ZHAI Hong

    2004-01-01

    Genetic diversity of 48 sweetpotato landraces randomly sampled from Anhui,Fujian, Henan and Guangdong provinces in China was analyzed using RAPD, ISSR and AFLP markers. Thirty RAPD primers, 14 ISSR primers and 9 AFLP primer pairs generated 227, 249 and 260 polymorphic bands, respectively. AFLP markers were better than RAPD and ISSR markers in terms of the number of polymorphic bands detected and the experimental stability. These three molecular markers revealed the similar results that Chinese landraces exhibited a high level of genetic diversity, and the genetic variation of Guangdong landraces was significantly higher than those of the landraces from the other three regions. These results supported the hypothesis that China was a secondary center of sweetpotato diversity. The present results also supported the view that sweetpotato was first introduced to Guangdong and from there spread to other regions of China. The dendrogram based on the combined RAPD, ISSR and AFLP dataset could separate the 48 landraces into two groups: One mainly including 8 landraces from Guangdong and the other consisting of the remaining landraces from Guangdong and landraces from the other three regions. Thus, the utilization of Guangdong landraces should be specially considered in sweetpotato breeding.

  7. Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

    Science.gov (United States)

    McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

    2012-05-01

    Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

  8. Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

    OpenAIRE

    Edwards, F.A.; D. P. Edwards; Larsen, T H; Hsu, W W; Benedick, S; Chung, A.; Vun Khen, C; Wilcove, D S; Hamer, K C

    2013-01-01

    Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. W...

  9. 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...... eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79......% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations....

  10. Genetic and Functional Diversity of Propagating Cells in Glioblastoma

    Directory of Open Access Journals (Sweden)

    Sara G.M. Piccirillo

    2015-01-01

    Full Text Available Glioblastoma (GBM is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo.

  11. Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

    Science.gov (United States)

    Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  12. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    Directory of Open Access Journals (Sweden)

    Spurthi N Nayak

    Full Text Available Sugarcane (Saccharum spp. and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1 genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2 form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.

  13. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    Science.gov (United States)

    Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.

  14. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).

    Science.gov (United States)

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.

  15. Diversity, abundance, and structure of tree communities in the Uluguru forests in the Morogoro region, Tanzania

    Institute of Scientific and Technical Information of China (English)

    David Sylvester Kacholi; Anthony Michael Whitbread; Martin Worbes

    2015-01-01

    Uluguru forests are globally recognized as important biodiversity hotspots, but anthropogenic pressure threatens their value. This study examined species diver-sity, abundance, and structure of trees in the Uluguru for-ests. All trees of diameter at breast height (DBH) C 10 cm were inventoried in seven forests ranging from 3 to 995 ha in area. A total of 900 stems, 101 species and 34 families were inventoried. Fabaceae was the most speciose family. Ehretia amoena Klotzsch was the most abundant species with relative abundance of 9.22%. The forests differed significantly in species richness (26–93 species ha-1), tree density (85–390 stems ha-1), basal area (3–24 m2 ha-1) and Shannon-Wiener diversity (2.50–4.02). Forest area was significantly and positively correlated with species richness (r=0.92) and species diversity (r=0.95). Tree density showed significant positive correlation with species richness (r=0.80) and basal area (r=0.85). Milawilila and Nemele forests had highest floristic similarity (0.55) followed by Kimboza and Kilengwe (0.54) while the rest had similarity coefficients of less than 0.50. Despite leg-islative protection, many forests remain at risk and there-fore the possibility to conserve highly valuable tree species via enhanced protection or cultivation must be considered.

  16. Floristic diversity in urban forest area of NEERI Campus, Nagpur, Maharashtra (India).

    Science.gov (United States)

    Gupta, Rakhi B; Chaudhari, P R; Wate, S R

    2008-01-01

    This study has been carried out to assess the diverse floristic wealth in urban forest area of NEERI campus at Nagpur, Maharashtra (India). This urban forest is ecologically important to maintain the atmospheric temperature around 2 degrees C below and higher relative humidity as compared to other urban areas. The water table is also observed to be shallower in this area as compared to other areas. Therefore, the biological diversity of this urban forest was studied, as it is directly related to ecology of the area. Floristic survey of NEERI premises recorded 135 vascular plants including 16 monocots and 119 dicots, belonging to 115 genera and 53 families. The taxa included 4 types of grasses, 55 herbs, 30 shrubs and 46 trees. The large number of species within very small area (43 ha) indicates rich biodiversity in this forest area. It is also observed that this forest patch has tall trees, with good density and rich cover of shrubs and herbs on forest floor indicating well knit plant community. These characteristics have given immense ecological importance to this urban forest area. Detailed vegetation study revealed that positive co-operation in the plant communities can significantly maintain species diversity in the environment.

  17. High bee and wasp diversity in a heterogeneous tropical farming system compared to protected forest.

    Directory of Open Access Journals (Sweden)

    Christof Schüepp

    Full Text Available It is a globally important challenge to meet increasing demands for resources and, at the same time, protect biodiversity and ecosystem services. Farming is usually regarded as a major threat to biodiversity due to its expansion into natural areas. We compared biodiversity of bees and wasps between heterogeneous small-scale farming areas and protected forest in northern coastal Belize, Central America. Malaise traps operated for three months during the transition from wet to dry season. Farming areas consisted of a mosaic of mixed crop types, open habitat, secondary forest, and agroforestry. Mean species richness per site (alpha diversity, as well as spatial and temporal community variation (beta diversity of bees and wasps were equal or higher in farming areas compared to protected forest. The higher species richness and community variation in farmland was due to additional species that did not occur in the forest, whereas most species trapped in forest were also found in farming areas. The overall regional species richness (gamma diversity increased by 70% with the inclusion of farming areas. Our results suggest that small-scale farming systems adjacent to protected forest may not only conserve, but even favour, biodiversity of some taxonomic groups. We can, however, not exclude possible declines of bee and wasp diversity in more intensified farmland or in landscapes completely covered by heterogeneous farming systems.

  18. High bee and wasp diversity in a heterogeneous tropical farming system compared to protected forest.

    Science.gov (United States)

    Schüepp, Christof; Rittiner, Sarah; Entling, Martin H

    2012-01-01

    It is a globally important challenge to meet increasing demands for resources and, at the same time, protect biodiversity and ecosystem services. Farming is usually regarded as a major threat to biodiversity due to its expansion into natural areas. We compared biodiversity of bees and wasps between heterogeneous small-scale farming areas and protected forest in northern coastal Belize, Central America. Malaise traps operated for three months during the transition from wet to dry season. Farming areas consisted of a mosaic of mixed crop types, open habitat, secondary forest, and agroforestry. Mean species richness per site (alpha diversity), as well as spatial and temporal community variation (beta diversity) of bees and wasps were equal or higher in farming areas compared to protected forest. The higher species richness and community variation in farmland was due to additional species that did not occur in the forest, whereas most species trapped in forest were also found in farming areas. The overall regional species richness (gamma diversity) increased by 70% with the inclusion of farming areas. Our results suggest that small-scale farming systems adjacent to protected forest may not only conserve, but even favour, biodiversity of some taxonomic groups. We can, however, not exclude possible declines of bee and wasp diversity in more intensified farmland or in landscapes completely covered by heterogeneous farming systems.

  19. The effects of restoring logged tropical forests on avian phylogenetic and functional diversity.

    Science.gov (United States)

    Cosset, Cindy C P; Edwards, David P

    2017-09-01

    Selective logging is the most prevalent land-use change in the tropics. Despite the resulting degradation of forest structure, selectively logged forests still harbor a substantial amount of biodiversity leading to suggestions that their protection is the next best alternative to conserving primary, old-growth forests. Restoring carbon stocks under Reducing Emissions from Deforestation and Forest Degradation (REDD+) schemes is a potential method for obtaining funding to protect logged forests, via enrichment planting and liberation cutting of vines. This study investigates the impacts of restoring logged forests in Borneo on avian phylogenetic diversity, the total evolutionary history shared across all species within a community, and on functional diversity, with important implications for the protection of evolutionarily unique species and the provision of many ecosystem services. Overall and understorey avifaunal communities were studied using point count and mist netting surveys, respectively. Restoration caused a significant loss in phylogenetic diversity and MPD (mean pairwise distance) leaving an overall bird community of less total evolutionary history and more closely related species compared to unlogged forests, while the understorey bird community had MNTD (mean nearest taxon distance) that returned toward the lower levels found in a primary forest, indicating more closely related species pairs. The overall bird community experienced a significant loss of functional strategies and species with more specialized traits in restored forests compared to that of unlogged forests, which led to functional clustering in the community. Restoration also led to a reduction in functional richness and thus niches occupied in the understorey bird community compared to unlogged forests. While there are additional benefits of restoration for forest regeneration, carbon sequestration, future timber harvests, and potentially reduced threat of forest conversion, this must be

  20. Considering Future Potential Regarding Structural Diversity in Selection of Forest Reserves.

    Science.gov (United States)

    Lundström, Johanna; Öhman, Karin; Rönnqvist, Mikael; Gustafsson, Lena

    2016-01-01

    A rich structural diversity in forests promotes biodiversity. Forests are dynamic and therefore it is crucial to consider future structural potential when selecting reserves, to make robust conservation decisions. We analyzed forests in boreal Sweden based on 17,599 National Forest Inventory (NFI) plots with the main aim to understand how effectiveness of reserves depends on the time dimension in the selection process, specifically by considering future structural diversity. In the study both the economic value and future values of 15 structural variables were simulated during a 100 year period. To get a net present structural value (NPSV), a single value covering both current and future values, we used four discounting alternatives: (1) only considering present values, (2) giving equal importance to values in each of the 100 years within the planning horizon, (3) applying an annual discount rate considering the risk that values could be lost, and (4) only considering the values in year 100. The four alternatives were evaluated in a reserve selection model under budget-constrained and area-constrained selections. When selecting young forests higher structural richness could be reached at a quarter of the cost over almost twice the area in a budget-constrained selection compared to an area-constrained selection. Our results point to the importance of considering future structural diversity in the selection of forest reserves and not as is done currently to base the selection on existing values. Targeting future values increases structural diversity and implies a relatively lower cost. Further, our results show that a re-orientation from old to young forests would imply savings while offering a more extensive reserve network with high structural qualities in the future. However, caution must be raised against a drastic reorientation of the current old-forest strategy since remnants of ancient forests will need to be prioritized due to their role for disturbance

  1. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications

    Science.gov (United States)

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide. PMID:28107530

  2. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    Science.gov (United States)

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  3. Effects of landscape design of forest reserves on Saproxylic beetle diversity.

    Science.gov (United States)

    Bouget, C; Parmain, G

    2016-02-01

    Increasing the density of natural reserves in the forest landscape may provide conservation benefits for biodiversity within and beyond reserve borders. We used 2 French data sets on saproxylic beetles and landscape cover of forest reserves (LCFR) to test this hypothesis: national standardized data derived from 252 assessment plots in managed and reserve stands in 9 lowland and 5 highland forests and data from the lowland Rambouillet forest, a forested landscape where a pioneer conservation policy led to creation of a dense network of reserves. Abundance of rare and common saproxylic species and total saproxylic species richness were higher in forest reserves than in adjacent managed stands only in highland forests. In the lowland regional case study, as LCFR increased total species richness and common species abundance in reserves increased. In this case study, when there were two or more reserve patches, rare species abundance inside reserves was higher and common species richness in managed stands was higher than when there was a single large reserve. Spillover and habitat amount affected ecological processes underlying these landscape reserve effects. When LCFR positively affected species richness and abundance in reserves or managed stands, >12-20% reserve cover led to the highest species diversity and abundance. This result is consistent with the target of 17% forested land area in reserves set at the Nagoya biodiversity summit in 2010. Therefore, to preserve biodiversity we recommend at least doubling the current proportion of forest reserves in European forested landscapes. © 2015 Society for Conservation Biology.

  4. GENETIC CONSEQUENCES OF SEED DISPERSAL IN THREE SYMPATRIC FOREST HERBS. I. HIERARCHICAL POPULATION-GENETIC STRUCTURE.

    Science.gov (United States)

    Williams, Charles F; Guries, Raymond P

    1994-06-01

    To examine the effects of seed dispersal on spatial genetic structure, we compare three sympatric species of forest herbs in the family Apiaceae whose fruits differ widely in morphological adaptations for animal-attached dispersal. Cryptotaenia canadensis has smooth fruits that are gravity dispersed, whereas Osmorhiza claytonii and Sanicula odorata fruits have appendages that facilitate their attachment to animals. The relative seed-dispersal ability among species, measured as their ability to remain attached to mammal fur, is ranked Sanicula > Osmorhiza > Cryptotaenia. We use a nested hierarchical sampling design to analyze genetic structure at spatial scales ranging from a few meters to hundreds of kilometers. Genetic differentiation among population subdivisions, estimated by average genetic distance and hierarchical F-statistics, has an inverse relationship with dispersal ability such that Cryptotaenia > Osmorhiza > Sanicula. In each species, genetic differentiation increases with distance among population subdivisions. Stochastic variation in gene flow, arising from seed dispersal by attachment to animals, may partly explain the weak relationship between pairwise spatial and genetic distance among populations and heterogeneity in estimates of single locus F-statistics. A hierarchical island model of gene flow is invoked to describe the effects of seed dispersal on population genetic structure. Seed dispersal is the predominant factor affecting variation in gene flow among these ecologically similar, taxonomically related species. © 1994 The Society for the Study of Evolution.

  5. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation.

    Science.gov (United States)

    Holmes, Christopher J; Pantel, Jelena H; Schulz, Kimberly L; Cáceres, Carla E

    2016-07-01

    When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.

  6. Woody species composition, diversity and structure of riparian forests of four watercourses types in Burkina Faso

    Institute of Scientific and Technical Information of China (English)

    Oumarou Sambaré; Fidèle Bognounou; Rüdiger Wittig; Adjima Thiombiano

    2011-01-01

    Riparian forests are classified as endangered ecosystems in general, particularly in sahelian countries like Burkina Faso because of human-induced alterations and civil engineering works. The modification of this important habitat is continuing, with little attention being paid to the ecological or human consequences of these changes. The objective of this study is to describe the variation of woody species diversity and dynamic in riparian forests on different type of watercourse banks along phytogeographical gradient in Burkina Faso. All woody species were systematically measured in 90 sample plots with sides of 50 m × 20 m.Density, dominance, frequency and species and family importance values were computed to characterize the species composition. Different diversity indices were calculated to examine the heterogeneity of riparian forests. A total of 196 species representing 139 genera and 51 families were recorded in the overall riparian forests. The species richness of individuals with dbh ≥ 5cm increased significantly from the North to the South along the phytogeographical gradient and varied significantly between the different types of riparian forests. Similarity in tree species composition between riparian forests was low, which indicates high beta diversity and reflects differences in habitat conditions and topography.The structural characteristics varied significantly along the phytogeographical gradient and between the different types of riparian forests.The diameter class distribution of trees in all riparian forests showed a reverse “J” shaped curve except riparian forest of stream indicating vegetation dominated by juvenile individuals. Considering the ecological importance of riparian forest, there is a need to delineate and classify them along watercourses throughout the country.

  7. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

    Directory of Open Access Journals (Sweden)

    Magdalena Szenejko

    2016-09-01

    Full Text Available Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA. Results The low value of Dice’s coefficient (0.369 along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

  8. Diversity, Stand Characteristics and Spatial Aggregation of Tree Species in a Bangladesh Forest Ecosystem

    Directory of Open Access Journals (Sweden)

    Carl Beierkuhnlein

    2011-08-01

    Full Text Available Assessing biodiversity and the spatial structures of forest ecosystems are important for forestry and nature conservation. However, tropical forests of Bangladesh are only sparsely investigated. Here we determined biodiversity (alpha, beta and gamma, spatial species turnover and stand characteristics of one of the few remnant tropical forests in Bangladesh. Two differently protected areas of Satchari forest were compared. We recorded tree species composition, in a systematic plot design, measured diameter at breast height for each individual tree (to assess basal area, and calculated decay in similarity of tree species composition with geographical distance. The distance-decay was assessed separately for the whole study area and for two subsamples from Satchari National Park and Satchari Reserve Forest. Satchari National Park (strictly protected had, despite its smaller area, a higher Alpha and Gamma diversity, but a lower Beta diversity than Satchari Reserve Forest. Variation in species composition was not significant between the two differently protected areas. Basal area increased significantly with protection status although tree individuals were of equal size in both areas. Plots in the Reserve Forest were associated with higher species turnover than in the National Park. We suggest anthropogenic disturbance, which occurs in the less strictly protected Reserve Forest, is the main driver for the detected spatial heterogeneity in species composition.

  9. Gene flow and genetic diversity in cultivated and wild cacao (Theobroma cacao) in Bolivia.

    Science.gov (United States)

    Chumacero de Schawe, Claudia; Durka, Walter; Tscharntke, Teja; Hensen, Isabell; Kessler, Michael

    2013-11-01

    The role of pollen flow within and between cultivated and wild tropical crop species is little known. To study the pollen flow of cacao, we estimated the degree of self-pollination and pollen dispersal distances as well as gene flow between wild and cultivated cacao (Theobroma cacao L.). We studied pollen flow and genetic diversity of cultivated and wild cacao populations by genotyping 143 wild and 86 cultivated mature plants and 374 seedlings raised from 19 wild and 25 cultivated trees at nine microsatellite loci. A principal component analysis distinguished wild and cultivated cacao trees, supporting the notion that Bolivia harbors truly wild cacao populations. Cultivated cacao had a higher level of genetic diversity than wild cacao, presumably reflecting the varied origin of cultivated plants. Both cacao types had high outcrossing rates, but the paternity analysis revealed 7-14% self-pollination in wild and cultivated cacao. Despite the tiny size of the pollinators, pollen was transported distances up to 3 km; wild cacao showed longer distances (mean = 922 m) than cultivated cacao (826 m). Our data revealed that 16-20% of pollination events occurred between cultivated and wild populations. We found evidence of self-pollination in both wild and cultivated cacao. Pollination distances are larger than those typically reported in tropical understory tree species. The relatively high pollen exchange from cultivated to wild cacao compromises genetic identity of wild populations, calling for the protection of extensive natural forest tracts to protect wild cacao in Bolivia.

  10. Functional diversity response to hardwood forest management varies across taxa and spatial scales.

    Science.gov (United States)

    Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A

    2017-03-15

    Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature-forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term dataset that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these datasets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting, while

  11. Genetic diversity and conservation of South African indigenous chicken populations.

    Science.gov (United States)

    Mtileni, B J; Muchadeyi, F C; Maiwashe, A; Groeneveld, E; Groeneveld, L F; Dzama, K; Weigend, S

    2011-06-01

    In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the

  12. Characterisation of the genetic diversity of Brucella by multilocus sequencing

    Directory of Open Access Journals (Sweden)

    MacMillan Alastair P

    2007-04-01

    Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

  13. Mitochondrial DNA diversity and population structure of a forest-dependent rodent, Praomys taitae (Rodentia: Muridae) Heller 1911, in the fragmented forest patches of Taita Hills, Kenya

    DEFF Research Database (Denmark)

    Nyakaana, S.; Tumusiime, C.; Oguge, N.;

    2008-01-01

    The population genetic structure of the forest-dependent rodent, Praomys taitae, sampled from nine indigenous forest fragments sampled from nine indigenous forest fragments distributed over three ranges of the Taita Hills in Kenya, was determined using mitochondrial DNA (mtDNA) control region...

  14. Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta

    Directory of Open Access Journals (Sweden)

    Chen Charlotte

    2012-06-01

    Full Text Available Abstract Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods. The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total was found for Spirogyra (41 NHS and for each clade (totaling 73 NHS. This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.

  15. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  16. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

    Directory of Open Access Journals (Sweden)

    Félix Marie-Anne

    2013-01-01

    Full Text Available Abstract Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and

  17. Tropical rain forest conservation and the twin challenges of diversity and rarity.

    Science.gov (United States)

    Hubbell, Stephen P

    2013-09-01

    Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.

  18. Lower within-community variance of negative density dependence increases forest diversity.

    Directory of Open Access Journals (Sweden)

    António Miranda

    Full Text Available Local abundance of adult trees impedes growth of conspecific seedlings through host-specific enemies, a mechanism first proposed by Janzen and Connell to explain plant diversity in forests. While several studies suggest the importance of this mechanism, there is still little information of how the variance of negative density dependence (NDD affects diversity of forest communities. With computer simulations, we analyzed the impact of strength and variance of NDD within tree communities on species diversity. We show that stronger NDD leads to higher species diversity. Furthermore, lower range of strengths of NDD within a community increases species richness and decreases variance of species abundances. Our results show that, beyond the average strength of NDD, the variance of NDD is also crucially important to explain species diversity. This can explain the dissimilarity of biodiversity between tropical and temperate forest: highly diverse forests could have lower NDD variance. This report suggests that natural enemies and the variety of the magnitude of their effects can contribute to the maintenance of biodiversity.

  19. Lower within-community variance of negative density dependence increases forest diversity.

    Science.gov (United States)

    Miranda, António; Carvalho, Luís M; Dionisio, Francisco

    2015-01-01

    Local abundance of adult trees impedes growth of conspecific seedlings through host-specific enemies, a mechanism first proposed by Janzen and Connell to explain plant diversity in forests. While several studies suggest the importance of this mechanism, there is still little information of how the variance of negative density dependence (NDD) affects diversity of forest communities. With computer simulations, we analyzed the impact of strength and variance of NDD within tree communities on species diversity. We show that stronger NDD leads to higher species diversity. Furthermore, lower range of strengths of NDD within a community increases species richness and decreases variance of species abundances. Our results show that, beyond the average strength of NDD, the variance of NDD is also crucially important to explain species diversity. This can explain the dissimilarity of biodiversity between tropical and temperate forest: highly diverse forests could have lower NDD variance. This report suggests that natural enemies and the variety of the magnitude of their effects can contribute to the maintenance of biodiversity.

  20. Genetic diversity in cattle of eight regions in Costa Rica.

    Directory of Open Access Journals (Sweden)

    Juan Miguel Cordero-Solórzano

    2015-06-01

    Full Text Available The aim of this study was to explore the extent of inter-regional genetic diversity present in the cattle of Costa Rica. 1498 DNA samples were collected (year 2013 from eight different regions within the country. Allelic frequencies and major population genetic parameters were determined for eighteen microsatellite markers. An analysis of molecular variance was also carried out and genetic distances were calculated between cattle from different regions. At the national level, a high allelic diversity was found, with an average of 14.6±1.01 observed alleles and 5.6+0.37 effective alleles per marker. Observed (Ho and expected (He heterozygosities were 0.76±0.01 and 0.81±01, respectively. Polymorphic Information Content (PIC and Coefficient of Inbreeding (FIS were 0.79±0.06 and 0.06±0.004, respectively. At the regional level, Ho ranged between 0.73±0.02 in the South Central region to 0.78±0.01 in the North Huetar region. The dendrogram showed three clearly distinct groups, Metropolitan Central and West Central regions in one group, Caribbean Huetar, South Central, Central Pacific and Chorotega regions in a second group; and North Huetar and Brunca regions in a third intermediate group. Estimates of genetic differentiation (RST were significant between regions from different groups and non-significant for regions within the same group. Genetic differences between regions are related to differential proliferation of breed groups based on their adaptability to the agro-ecological conditions and production systems prevailing in each region.

  1. Species Diversity Based on Vertical Structure as Indicators of Artificial Restoration for Coniferous Forests in Southwest China

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qiaoying; ZHANG Yunchun; Eshetu Yirdaw; LUO Peng; YI Shaoliang; Wu Ning

    2006-01-01

    Five indices of species richness, species diversity and species evenness were used to assess α diversity of four types of coniferous forests undergone different artificial regeneration time. The study was based on the vertical structure of forests, involving growth-forms of total plants as well as vertical layers of woody plants. The results showed that, except for the fourth layer of woody plants, the vertical structure of the four forests exhibited significant difference in terms of their species richness, species diversity and species evenness, suggesting that α species diversity index provided more detailed information and was a better index reflecting the regeneration processes in this region. It was recommended that silvicultural management of artificially regenerated forests should be strengthened to conserve the biodiversity of the forests, optimize forest structure and, in the long run, promote sustainable development of forest ecosystems.

  2. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    Science.gov (United States)

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  3. Molecular assessment of genetic diversity in mung bean germplasm

    Indian Academy of Sciences (India)

    G. Roopa Lavanya; Jyoti Srivastava; Shirish A. Ranade

    2008-04-01

    RAPD profiles were used to identify the extent of diversity among 54 accessions of mung bean that included both improved and local land races. Out of the 40 primers screened, seven primers generated 174 amplification products with an average of 24.85 bands per primer. The RAPD profiles were analysed for Jaccard’s similarity coefficients that was found to be in the range from 0 to 0.48, indicating the presence of wide range of genetic diversity at molecular level. Cluster analysis was carried out based on distances (1-similarity coefficient) using neighbour-joining method in Free Tree package. The dendrogram resolved all the accessions into two major clusters, I (with 11 accessions) and II (with 43 accessions). However, the cluster was further divided into four subclusters (II A with six, II B with nine, II C with 15 and II D with 13 accessions). The distribution of the accessions in different clusters and subclusters appeares to be related to their performance in field conditions for 10 morphological traits that were scored. This study indicated that the RAPD profiles provide an easy and simple technique for preliminary genetic diversity assessment of mung bean accessions that may reflect morphological trait differences among them.

  4. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    Science.gov (United States)

    Menzies, Brandon R; Renfree, Marilyn B; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B; Pask, Andrew J

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

  5. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    Directory of Open Access Journals (Sweden)

    Brandon R Menzies

    Full Text Available The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

  6. Genetic diversity and molecular evolution of Chinese waxy maize germplasm.

    Directory of Open Access Journals (Sweden)

    Hongjian Zheng

    Full Text Available Waxy maize (Zea mays L. var. certaina Kulesh, with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima's D and Fu and Li's F* were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.

  7. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

    Directory of Open Access Journals (Sweden)

    Dong Hwan Lee

    2014-06-01

    Full Text Available The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed.

  8. 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...

  9. Tree species diversity mitigates disturbance impacts on the forest carbon cycle.

    Science.gov (United States)

    Pedro, Mariana Silva; Rammer, Werner; Seidl, Rupert

    2015-03-01

    Biodiversity fosters the functioning and stability of forest ecosystems and, consequently, the provision of crucial ecosystem services that support human well-being and quality of life. In particular, it has been suggested that tree species diversity buffers ecosystems against the impacts of disturbances, a relationship known as the "insurance hypothesis". Natural disturbances have increased across Europe in recent decades and climate change is expected to amplify the frequency and severity of disturbance events. In this context, mitigating disturbance impacts and increasing the resilience of forest ecosystems is of growing importance. We have tested how tree species diversity modulates the impact of disturbance on net primary production and the total carbon stored in living biomass for a temperate forest landscape in Central Europe. Using the simulation model iLand to study the effect of different disturbance regimes on landscapes with varying levels of tree species richness, we found that increasing diversity generally reduces the disturbance impact on carbon storage and uptake, but that this effect weakens or even reverses with successional development. Our simulations indicate a clear positive relationship between diversity and resilience, with more diverse systems experiencing lower disturbance-induced variability in their trajectories of ecosystem functioning. We found that positive effects of tree species diversity are mainly driven by an increase in functional diversity and a modulation of traits related to recolonization and resource usage. The results of our study suggest that increasing tree species diversity could mitigate the effects of intensifying disturbance regimes on ecosystem functioning and improve the robustness of forest carbon storage and the role of forests in climate change mitigation.

  10. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  11. Contributions of a global network of tree diversity experiments to sustainable forest plantations.

    Science.gov (United States)

    Verheyen, Kris; Vanhellemont, Margot; Auge, Harald; Baeten, Lander; Baraloto, Christopher; Barsoum, Nadia; Bilodeau-Gauthier, Simon; Bruelheide, Helge; Castagneyrol, Bastien; Godbold, Douglas; Haase, Josephine; Hector, Andy; Jactel, Hervé; Koricheva, Julia; Loreau, Michel; Mereu, Simone; Messier, Christian; Muys, Bart; Nolet, Philippe; Paquette, Alain; Parker, John; Perring, Mike; Ponette, Quentin; Potvin, Catherine; Reich, Peter; Smith, Andy; Weih, Martin; Scherer-Lorenzen, Michael

    2016-02-01

    The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and disadvantages of mixed species plantations. The network currently consists of 18 experiments, distributed over 36 sites and five ecoregions. With plantations 1-15 years old, TreeDivNet can already provide relevant data for forest policy and management. In this paper, we highlight some early results on the carbon sequestration and pest resistance potential of more diverse plantations. Finally, suggestions are made for new, innovative experiments in understudied regions to complement the existing network.

  12. Overstory structure and soil nutrients effect on plant diversity in unmanaged moist tropical forest

    Science.gov (United States)

    Gautam, Mukesh Kumar; Manhas, Rajesh Kumar; Tripathi, Ashutosh Kumar

    2016-08-01

    Forests with intensive management past are kept unmanaged to restore diversity and ecosystem functioning. Before perpetuating abandonment after protracted restitution, understanding its effect on forest vegetation is desirable. We studied plant diversity and its relation with environmental variables and stand structure in northern Indian unmanaged tropical moist deciduous forest. We hypothesized that post-abandonment species richness would have increased, and the structure of contemporary forest would be heterogeneous. Vegetation structure, composition, and diversity were recorded, in forty 0.1 ha plots selected randomly in four forest ranges. Three soil samples per 0.1 ha were assessed for physicochemistry, fine sand, and clay mineralogy. Contemporary forest had less species richness than pre-abandonment reference period. Fourteen species were recorded as either seedling or sapling, suggesting reappearance or immigration. For most species, regeneration was either absent or impaired. Ordination and multiple regression results showed that exchangeable base cations and phosphorous affected maximum tree diversity and structure variables. Significant correlations between soil moisture and temperature, and shrub layer was observed, besides tree layer correspondence with shrub richness, suggesting that dense overstory resulting from abandonment through its effect on soil conditions, is responsible for dense shrub layer. Herb layer diversity was negatively associated with tree layer and shrub overgrowth (i.e. Mallotus spp.). Protracted abandonment may not reinforce species richness and heterogeneity; perhaps result in high tree and shrub density in moist deciduous forests, which can impede immigrating or reappearing plant species establishment. This can be overcome by density/basal area reduction strategies, albeit for both tree and shrub layer.

  13. Towards an understanding of tree diversity in Amazonian forests

    NARCIS (Netherlands)

    Stropp Carneiro, J.

    2011-01-01

    Amazonian forests harbor the highest biodiversity of all terrestrial ecosystems on Earth. The origin of this extraordinary biodiversity and its current distribution are recently becoming better understood. Still, our knowledge of the contribution of processes operating at different temporal and spat

  14. 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

  15. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils

    DEFF Research Database (Denmark)

    Priemé, Anders; Braker, Gesche; Tiedje, James M.

    2002-01-01

    The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from...... the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one...... marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall...

  16. The Diversity and Abundance of Springtail (Collembola on Forests and Smallholder in Jambi

    Directory of Open Access Journals (Sweden)

    Widrializa

    2015-09-01

    Full Text Available Harapan forests is the first restoration forest in Indonesia, includes several different ecosystems. Different ecosystems have different characteristic to affect the diversity and abundance of Collembola. In the ecosystem, Collembola have an important role in biocontrol, decomposition, soil nutrient distribution, stimulation of soil microbial activity and as an alternative feed for predators. This study was aimed to investigate the diversity and abundance of Collembola in four ecosystems at Harapan forest, i.e. secondary forest, rubber forest, rubber smallholder and oil palm smallholder. To achieve the objective, soil samples were taken at 48 observation points in the four ecosystem. The soil samples were then extracted by Kempson Extractor. The diversity and abundance of Collembola in four ecosystems were categorized as medium to high. The total of individual and population of Collembola in the secondary and rubber forest ecosystems were likely to be higher than in the rubber and oil palm smallholders. This study had also identified four orders, 14 families and 31 genera of Collembola, where Isotomiella and Proisotoma dominated the genus of Collembola in the four ecosystems.

  17. Taxonomic Diversity of Lianas in Tropical Forests of Northern Eastern Ghats of Andhra Pradesh, India

    Directory of Open Access Journals (Sweden)

    Maradana TARAKESWARA NAIDU

    2014-03-01

    Full Text Available Lianas are important in forest ecosystem and strongly influence the forest dynamics and diversity. Lianas are common in the tropical moist deciduous and rain forests, which are competing with other forest trees. Little information is known on the habitat specialization in tropical lianas diversity and the root causes for variation among forests in liana species composition. A total of 170 liana species (≥ 1.5 cm girth at breast height representing 109 genera and 43 families were reported in 5×5 m quadrate samples along with their climbing modes in the tropical forests of northern Eastern Ghats of Andhra Pradesh, India. A total of 210 grids were sampled in study area and reported that Convolvulaceae was the dominant family with 23 species followed by Papilionaceae, 22 species and Asclepiadaceae, 19 species and Ipomoea was the largest genera. Woody lianas were dominated by 128 species and these are classified into six climbing modes consisting in stem climbers (53.5% that were the most predominant followed by stragglersunarmed (14.7%, stragglers armed and tendril climbers (13.5% each, root climbers (2.9% and hook climbers (1.8%. The most dominant liana species in the northern Eastern Ghats were Acacia sinuata and Bauhinia vahlii. The results of this investigation suggests that better management and protection is an important for in situ conservation of liana diversity and involving local people is emphasized.

  18. Comparative Analysis of Plant Diversity of Pinus tabulaeformis Forests in Ten Regions of Beijing Mountainous Areas

    Institute of Scientific and Technical Information of China (English)

    Li Liping; Xing Shaohua; Zhao Bo; Wang Qingchun; Cui Guofa

    2006-01-01

    Based on investigations during 1998-2003,shrubs and herbs,as well as indicators of similarity and diversity in Pinus tabulaeformis forests of ten regions around Beijing were compared and analyzed,and protection measures were suggested.Generally,the shrubs and herbs in P.tabulaeformis forests of Shidu,Mutianyu,and Yunfengshan are rich in species diversity and have great similarities.The percentages of common species in each of these three paired regions are above 50%,while many peculiar plant species that could not be found in the other nine regions exist in Labagoumen.As for plant diversity indices,plants in the P.tabulaeformis forests of Baihuashan,Shidu,and Labagoumen occur more frequently than in other regions,while the number of plants in Tanjiesi and Miaofengshan are far less.Some endangered orchid species were found distributed in P.tabulaeformis forests with a clumped spatial pattern but rarely appeared in other forest types,indicating that P.tabulaeformis forests are ideal habitats for orchid species.

  19. Diversity and similarity of native forest fragments located in the northeast region of Minas Gerais

    Directory of Open Access Journals (Sweden)

    Christianne Riquetti Corsini

    2014-03-01

    Full Text Available In this study 26 distributed fragments of native forest in four located hydrographical Basins in the northeast region of Minas Gerais had been showed, with the purpose of analyzing the floristic similarity exists between 26 forest fragments native inserted in four basins in the northeast of the state of Minas Gerais and the diversity and evenness of physiognomies studied and groups of fragments formed. Systematic sampling with units was used shows of 1000 m² each, where the sample area varied of 1 the 6 has, as the area I break up of it. We measured the circumference at 1.30m (CAP and the total height and collected botanical material of all individuals with CAP greater or equal to 15.7 cm. Six groups were formed according to the floristic similarity coefficient Sorensen, with four groups there was an association of more than a physiognomy, showing regions of transition within the area. The Shannon diversity index, ranged from 2.236 in deciduous forest to 4.523 in Semideciduous Forest. The maximum and minimum values of evenness index Pielou were 0.850 and 0.616 , respectively. The floristic group 2 (Semideciduous Forest and Cerrado sensu stricto had the highest average value of diversity (3.585 and evenness (0.750 , and group 1 (Deciduous Forest had the lowest values (H': 2.426 and J': 0.687 .

  20. The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps.

    Science.gov (United States)

    Mosca, E; Eckert, A J; Di Pierro, E A; Rocchini, D; La Porta, Nicola; Belletti, P; Neale, D B

    2012-11-01

    Climate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay, single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua Mill., Pinus cembra L. and Pinus mugo Turra, across their natural ranges in the Italian Alps and Apennines. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified three to five genetic groups per species. Geographical correlates with these patterns, however, were only apparent for P. cembra. Multivariate environmental variables [i.e. principal components (PCs)] were subsequently tested for association with SNPs using a Bayesian generalized linear mixed model. The majority of the SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated with PC1, corresponding to winter precipitation and seasonal minimum temperature. In A. alba, four SNPs were associated with PC2, corresponding to the seasonal minimum temperature. Functional annotation of those genes with the orthologs in Arabidopsis revealed several genes involved in abiotic stress response. This study provides a detailed assessment of population structure and its association with environment and geography in four coniferous species in the Italian mountains.

  1. DIVERSITY, STRUCTURAL PARAMETERS AND NON-TIMBER FOREST PRODUCTS IN THE FOREST RESERVE OF BONEPOUPA (DOUALA, CAMEROON

    Directory of Open Access Journals (Sweden)

    Jean Paul Kamdem

    2013-12-01

    Full Text Available http://dx.doi.org/10.5902/1980509812363In order to come up with a sustainable use of forest ecosystems in Cameroon, its vegetal diversity has been inventoried; the plant potentials and the structural parameters were studied in the forest reserve of Bonepoupa. Ten non-continuous plots of 200 m² were done and the materialization of the lines was done with a topofil put at the centre of the field with ropes at 5 m each of the topofil. In addition, ninety people were interviewed in order to know the potential use of species in this region. Up to 172 individuals with Diameter at Breast Height (DBH ≥ 5 cm divided into 27 species, 25 genera and 18 families were inventoried and the coefficient of abundance-dominance was determined. The diversity index of Shannon (H’ was H’1 = 4.17 ± 0.45 with H’1max = 4.75 and the evenness was R1 = 0.88. Taking into account herbaceous species, H’ determined by the coefficient of abundance-dominance was H’2 = 4.74 ± 0.56 with H’2max = 5.70 and the evenness  was  R2 = 0.83. The  total  basal  area  was 19.69 m2/ha and the density was 860 individuals/ha. These results indicate that herbaceous significantly modifies the value of the diversity index and that forest reserve of Bonepoupa is experiencing a problem of conservation which is due to a lack of its appropriate management. The knowledge of non-timber forest products and their use as food as well as medicinal resources by local population might be helpful for the sustainable management of resources in this forest reserve.

  2. A Study on Forest Species Diversity and Its Ecological Service Function in the Plateau Area of Western Sichuan

    Institute of Scientific and Technical Information of China (English)

    Deng Yu-lin; Wang Yu-kuan; Peng Pei-hao

    2003-01-01

    This paper presents a study on species diversity and its ecological service function in the plateau area in western Sichuan. The results show that species diversity in the plantations on the cutover land has a tendency to increase and that its ecological service function is to be improved with stand age growing. The species diversity in forest communities is also gradually increased on different succession stage till reaching a climax level. But the species diversity in the climax community is slightly decreased before it reaches a relatively constant status. Ecological service function of diversity is gradually strengthened with the progress of succession. In addition, species diversity in a stand in a similar site and at a same age differs among forest types. Species diversity index within a coniferous and broad-leaved mixed forest is larger than that within a coniferous forest. Meanwhile, species diversity enriches as the tree density increases.

  3. [Distribution of the genetic diversity of the Siberian stone pine, Pinus sibirica Du Tour, along the latitudinal and longitudinal profiles].

    Science.gov (United States)

    Petrova, E A; Goroshkevich, S N; Belokon', M M; Belokon', Iu S; Politov, D V

    2014-05-01

    The Siberian stone pine (Pinus sibirica Du Tour) is one of the main forest-forming coniferous species of the boreal ecosystems of Western Siberia. We used the isozyme method to analyze 11 ecotypes representing the latitudinal and longitudinal profiles within the species range, including samples from the geographic boundaries of the distribution. The genetic structure of the ecotypes is described on the basis of the variability for 26 isozyme loci encoding for 16 enzyme systems. The greatest genetic diversity was observed in the taiga ecotypes in the central part of the studied area, while the ecotypes along the species range boundaries were shown to be genetically depauperized. Approximately 8.1% of the observed genetic diversity is attributed to differences between the studied ecotypes. We detected high levels of genetic diversity for the Fest_2, Pgm_1, Sod_4, and a few otherloci, as well as a correlation between allele frequencies and geographical locations of the populations. The results of multivariate analysis of allelic frequencies as well as cluster analysis allowed us to discriminate three major groups of ecotypes: north-eastern, central and south-western. In view of our results, we compare two hypotheses: one which attributes the spatial distribution of genetic variations to the selectivity for some of the polymorphic allozyme loci, and the other based in the history of the formation of the range of the Siberian stone pine.

  4. Terrestrial mammal diversity in forests close to pineapple crops, Cutris San Carlos, Costa Rica.

    OpenAIRE

    2015-01-01

    Pineapple crops reduce the size of forest fragments and generate pressure on biodiversity in the remnants. To determine potential negative effects of forest fragmentation we assessed diversity and composition of terrestrial mammals in forest patches on three farms under pineapple crops. We placedSherman and Tomahawk traps, footprints traps near water bodies, and made daily tracks to obtain traces and direct observation of mammals. We identified seven species of wild mammals, mostly omnivorous...

  5. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    Directory of Open Access Journals (Sweden)

    Olav Rueppell

    Full Text Available Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  6. Faunal diversity of Fagus sylvatica forests: A regional and European perspective based on three indicator groups

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    H. Walentowski

    2014-12-01

    Full Text Available While the postglacial history of European beech (Fagus sylvatica and the plant species composition of beech forests in  Central Europe are fairly well understood, the faunal biodiversity has been less well investigated. We studied three groups of  mostly sedentary organisms in beech forest at regional and European scales by combining field studies with a compilation of existing literature and expert knowledge. Specifically, we examined the relationship between host tree genera and saproxylic  beetles, and the diversity and composition of forest ground-dwelling molluscs and ground beetles in relation to the abundance  of beech. At a west central European scale (Germany, where beech has a “young” ecological and biogeographical history,  we found 48 primeval forest relict species of saproxylic beetles associated with beech, 124 ground beetles and 91 molluscs  inhabiting beech forest, yet none exclusive of west central European beech forests. High levels of faunal similarity between beech and other woodland trees suggested that many of the beech forest dwelling species are euryoecious and likely to  originate from mid-Holocene mixed broadleaf forests. Beech forests of the mountain ranges in southern and east central  Europe, which are ecologically and biogeographically “old”, were found to harbour distinct species assemblages, including  beech forest specialists (such as 10 carabid species in the Carpathians and narrow-range endemics of broadleaf forest. The  observed biodiversity patterns suggest differentiated conservation priorities in “young” and “old” European beech forest  regions.

  7. Diversity Controlling Genetic Algorithm for Order Acceptance and Scheduling Problem

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    Cheng Chen

    2014-01-01

    Full Text Available Selection and scheduling are an important topic in production systems. To tackle the order acceptance and scheduling problem on a single machine with release dates, tardiness penalty, and sequence-dependent setup times, in this paper a diversity controlling genetic algorithm (DCGA is proposed, in which a diversified population is maintained during the whole search process through survival selection considering both the fitness and the diversity of individuals. To measure the similarity between individuals, a modified Hamming distance without considering the unaccepted orders in the chromosome is adopted. The proposed DCGA was validated on 1500 benchmark instances with up to 100 orders. Compared with the state-of-the-art algorithms, the experimental results show that DCGA improves the solution quality obtained significantly, in terms of the deviation from upper bound.

  8. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  9. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.

    Science.gov (United States)

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.

  10. Metabolic diversity and microbial biomass in forest soils across climatic and tree species diversity gradients

    OpenAIRE

    Carnol, Monique; Bosman, Bernard; Vanoppen, Astrid; De Wandeler, Hans; Muys, Bart

    2013-01-01

    The biogeochemical cycling in forest ecosystems is highly dependent on the interactions between plants and soil. Tree species affect element cycling through deposition in throughfall, litterfall, microbial activities in soil and rhizosphere processes. Tree species diversification has been suggested for maintaining forest ecosystem services and combining provisioning and supporting services within multifunctional and sustainable forestry. However, the understanding of the role of biodiversity ...

  11. Genetic diversity in populations of Gentoo penguins (Pygoscelis papua).

    Science.gov (United States)

    Dranitsina, A S; Telegeev, G D; Maliuta, S S; Bezrukov, V F

    2006-01-01

    RAPD analysis was used to examine the extent of genetic polymorphism in two populations of Gentoo penguin (Pygoscelis papua) from Antarctic Islands (Petermann and Livingston). The chosen two of three 10 mer oligonucleotide primers accordingly to preliminary results showed different levels of polymorphism in Gentoo penguins at Petermann Island (from 23.53 to 42.86%) and Livingston Island (from 52.94 to 57.14%). Nei's similarity coefficients were in range from 0.5606 (when Gentoo genome profiles were compared with RAPD profiles of two related penguin species: Pygoscelis adeliae (Adelie) and Pygoscelis antarctica (Chinstrep)) to 0.9281 among observed Gentoo penguin populations. Nei's distances values ranged from 0.0746 to 0.5787 among the populations and species. The obtained results will be used for further estimation of genetic diversity of Gentoo penguins and determination of their taxonomic status.

  12. The impact of recent events on human genetic diversity.

    Science.gov (United States)

    Jobling, Mark A

    2012-03-19

    The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.

  13. Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey

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    Zafer Bulut

    2016-01-01

    Full Text Available The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P0.05. Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers.

  14. ISSR markers for analysis of molecular diversity and genetic structure of Indian teak (Tectona grandis L.f. populations

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    S.A. Ansari

    2012-05-01

    Full Text Available Inter simple sequence repeats (ISSR constitute a powerful dominantDNA molecular marker system used for diversity analysis, which isindispensable for making estimates of genetic base and demarcation of populations for undertaking conservation and improvement program of forest tree species. Twenty nine populations of teak (Tectona grandis L.f. were collected from central and peninsular India for analysis of genetic diversity and structure. Genomic DNA from ten randomly selected individuals of each population was extracted and amplified using five ISSR primers(UBC-801, 834, 880, 899 and 900. The primers showed 100% polymorphism. UBC-900 recorded the highest Nei’s genetic diversity (0.32 to 0.40and UBC-899 had the highest Shannon’s Information Index (0.49 to 0.59. AMOVA revealed a very high intra-population genetic diversity (91%, in comparison to inter-population genetic diversity among states (6.17% and within states (2.77% which were also indirectly confirmed by large standard deviations associated with genetic diversity estimates for individual population, as well as poor bootstrapping values for most of the cluster nodes. However, UPGMA dendrogram revealed several clusters, with populationsfrom central India being present almost in each cluster, makinggroups with populations of adjoining states and distant states. Nevertheless,the cluster analysis distinguished the drier teak populations of central India from the moist teak populations of south India, which was also confirmed by Principle Coordinate Analysis. The findings advocates the need not only for enhancing selection intensity for large number of plus trees, but also for laying out more number of in situ conservation plots within natural populations of each cluster for germplasm conservation of teak aimed at improving the teak productivity and quality in future.

  15. Centennial olive trees as a reservoir of genetic diversity

    Science.gov (United States)

    Díez, Concepción M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

    2011-01-01

    Background and Aims Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. Methods The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Key Results Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. Conclusions This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity. PMID:21852276

  16. Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses.

    Science.gov (United States)

    Higgins, K Lindsay; Coley, Phyllis D; Kursar, Thomas A; Arnold, A Elizabeth

    2011-01-01

    Most studies examining endophytic fungi associated with grasses (Poaceae) have focused on agronomically important species in managed ecosystems or on wild grasses in subtropical, temperate and boreal grasslands. However grasses first arose in tropical forests, where they remain a significant and diverse component of understory and forest-edge communities. To provide a broader context for understanding grass-endophyte associations we characterized fungal endophyte communities inhabiting foliage of 11 species of phylogenetically diverse C(3) grasses in the understory of a lowland tropical forest at Barro Colorado Island, Panama. Our sample included members of early-arising subfamilies of Poaceae that are endemic to forests, as well as more recently arising subfamilies that transitioned to open environments. Isolation on culture media and direct PCR and cloning revealed that these grasses harbor species-rich and phylogenetically diverse communities that lack the endophytic Clavicipitaceae known from diverse woodland and pasture grasses in the temperate zone. Both the incidence and diversity of endophytes was consistent among grass species regardless of subfamily, clade affiliation or ancestral habitat use. Genotype and phylogenetic analyses suggest that these endophytic fungi are predominantly host generalists, shared not only among distinctive lineages of Poaceae but also with non-grass plants at the same site.

  17. Frankia and Alnus rubra canopy roots: an assessment of genetic diversity, propagule availability, and effects on soil nitrogen.

    Science.gov (United States)

    Kennedy, Peter G; Schouboe, Jesse L; Rogers, Rachel H; Weber, Marjorie G; Nadkarni, Nalini M

    2010-02-01

    The ecological importance of microbial symbioses in terrestrial soils is widely recognized, but their role in soils that accumulate in forest canopies is almost entirely unknown. To address this gap, this study investigated the Frankia-Alnus rubra symbiosis in canopy and forest floor roots at Olympic National Park, WA, USA. Sixteen mature A. rubra trees were surveyed and Frankia genetic diversity in canopy and forest floor nodules was assessed with sequence-based nifH analyses. A seedling bioassay experiment was conducted to determine Frankia propagule availability in canopy and forest floor soils. Total soil nitrogen from both environments was also quantified. Nodules were present in the canopies of nine of the 16 trees sampled. Across the study area, Frankia canopy and forest floor assemblages were similar, with both habitats containing the same two genotypes. The composition of forest floor and canopy genotypes on the same tree was not always identical, however, suggesting that dispersal was not a strictly local phenomenon. Frankia seedling colonization was similar in canopy soils regardless of the presence of nodules as well as in forest floor soils, indicating that dispersal was not likely to be a major limiting factor. The total soil nitrogen of canopy soils was higher than that of forest floor soils, but the presence of Frankia nodules in canopy soils did not significantly alter soil nitrogen levels. Overall, this study indicates that the Frankia-A. rubra symbiosis is similar in canopy and forest floor environments. Because canopy roots are exposed to different environmental conditions within very small spatial areas and because those areas can be easily manipulated (e.g., fertilizer or watering treatments), they present microbial ecologists with a unique arena to examine root-microbe interactions.

  18. Evaluation of nine distance-based measures of functional diversity applied to forest communities

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    Jin-Tun Zhang

    2013-05-01

    Full Text Available Several methods for the estimation of functional diversity are employed in plant communities. However, it is hard to select the most suitable measures in practice. This work presents comparisons of nine distance-based measures applied to functional diversity analysis in forest communities (36m plots along an elevational gradient in the Pangquangou Reserve, China. The employed indices and methods were: functional attribute diversity (FAD, Rao’s functional diversity (Rao’s index, single linkage (SL, complete linkage (CL, Unweighted Pair Group Method with Arithmetic Mean (UPGMA, Unweighted Pair-Group Method using Centroids (UPGMC, Median linkage (Median, fuzzy equivalence diversity (Fuzzy index and minimum spanning tree index (MST. The results showed that all the nine measures successfully quantified the functional diversity in plant communities and described the changes along environmental gradient. It was concludedthat all the employed indices and methods were equally effectiveand significantly correlated. Comparatively, fuzzy index, MST, UPGMC,UPGMA and Median were more suitable and should have priority over theother four measures in functional diversity analysis. A combination of a few measures of functional diversity within the same study was recommended. Functional diversity indices were significantly decreasing with elevation and correlated with species richness in the studied forest communities.

  19. Evaluation of nine distance-based measures of functional diversity applied to forest communities

    Directory of Open Access Journals (Sweden)

    Jin-Tun Zhang

    2013-07-01

    Full Text Available Several methods for the estimation of functional diversity are employed in plant communities. However, it is hard to select the most suitable measures in practice. This work presents comparisons of nine distance-based measures applied to functional diversity analysis in forest communities (36 plots along an elevational gradient in the Pangquangou Reserve, China. The employed indices and methods were: functional attribute diversity (FAD, Rao’s functional diversity (Rao’s index, single linkage (SL, complete linkage (CL, Unweighted Pair Group Method with Arithmetic Mean (UPGMA, Unweighted Pair-Group Method using Centroids (UPGMC, Median linkage (Median, fuzzy equivalence diversity (Fuzzy index and minimum spanning tree index (MST. The results showed that all the nine measures successfully quantified the functional diversity in plant communities and described the changes along environmental gradient. It was concluded that all the employed indices and methods were equally effective and significantly correlated. Comparatively, fuzzy index, MST, UPGMC, UPGMA and Median were more suitable and should have priority over the other four measures in functional diversity analysis. A combination of a few measures of functional diversity within the same study was recommended. Functional diversity indices were significantly decreasing with elevation and correlated with species richness in the studied forest communities. 

  20. Effects of experimental nitrogen additions on plant diversity in tropical forests of contrasting disturbance regimes in southern China

    Energy Technology Data Exchange (ETDEWEB)

    Lu Xiankai [Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510160 (China); Mo Jiangming, E-mail: mojm@scib.ac.cn [Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510160 (China); Gilliam, Frank S. [Department of Biological Sciences, Marshall University, Huntington, WV 25755-2510 (United States); Yu Guirui [Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101 (China); Zhang Wei; Fang Yunting; Huang Juan [Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510160 (China)

    2011-10-15

    Responses of understory plant diversity to nitrogen (N) additions were investigated in reforested forests of contrasting disturbance regimes in southern China from 2003 to 2008: disturbed forest (with harvesting of understory vegetation and litter) and rehabilitated forest (without harvesting). Experimental additions of N were administered as the following treatments: Control, 50 kg N ha{sup -1} yr{sup -1}, and 100 kg N ha{sup -1} yr{sup -1}. Nitrogen additions did not significantly affect understory plant richness, density, and cover in the disturbed forest. Similarly, no significant response was found for canopy closure in this forest. In the rehabilitated forest, species richness and density showed no significant response to N additions; however, understory cover decreased significantly in the N-treated plots, largely a function of a significant increase in canopy closure. Our results suggest that responses of plant diversity to N deposition may vary with different land-use history, and rehabilitated forests may be more sensitive to N deposition. - Highlights: > Nitrogen addition had no significant effect on understory plant diversity in the disturbed forest. > Nitrogen addition significantly decreased understory plant cover. > Nitrogen addition had no effect on richness and density in the rehabilitated forest. > The decrease is largely a function of a significant increase in canopy closure. > Land-use practices may dominate the responses of plant diversity to N addition. - Research in disturbed forests of southeastern China demonstrates that land-use history can substantially alter effects of excess nitrogen deposition on plant diversity of tropical forest ecosystems.

  1. Arthropod diversity in pure oak forests of coppice origin in northern Thrace (Turkey

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    Keten A

    2015-10-01

    Full Text Available Oak (Quercus spp. forests are among the most important forest types in Turkey. In the past, oak forests were managed through coppice clear-cutting, but in recent decades they have mostly been converted to high forest. This study was aimed at explaining how arthropod diversity is affected during conversion from coppice to high oak forest and during the early stages of coppice succession. We tested the hypothesis that arthropod richness, abundance and diversity in coppice oak sites varied according to stand age and a number of other forest characteristics. Arthropod communities were sampled in 50 plots using four different methods: pitfall traps, sweep nets, sticky cards and cloth shaking. A total of 13 084 individuals were collected and classified into 193 Recognizable Taxonomic Units (RTUs, with the most RTUs and the greatest number of specimens captured by sweep netting. We identified 17 taxa within RTU’s with more than 1% of the captured arthropods, which constituted 75% of the total specimens. The number of RTUs varied significantly according to trap type. Arthropod richness and Shannon-Wiener biodiversity index (H′ increased with elevation and precipitation. In young (1-40 yrs-old and middle-aged (41-80 yrs stands, arthropod biodiversity was not significantly affected by stand type, but slightly increased with diameter at breast height and tree height. Forest characteristics, such as the litter layer, understory and crown diameter, weakly influenced arthropod richness and abundance. Cluster analysis revealed that stand types and trap types differed taxonomically. Principal component analysis showed that stand types were clearly separated by the stand parameters measured. Insect families (Formicidae, Thripidae, Lygaeidae, Dolichopodidae, Luaxanidae, Cicadellidae and Ichneumonidae could potentially be used as indicators of coppice oak conditions. As the coppice oak changes to mature forest, further studies are needed to better assess the

  2. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

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    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  3. On the Biological and Genetic Diversity in Neospora caninum

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    John T. Ellis

    2010-03-01

    Full Text Available Neospora caninum is a parasite regarded a major cause of foetal loss in cattle. A key requirement to an understanding of the epidemiology and pathogenicity of N. caninum is knowledge of the biological characteristics of the species and the genetic diversity within it. Due to the broad intermediate host range of the species, worldwide geographical distribution and its capacity for sexual reproduction, significant biological and genetic differences might be expected to exist. N. caninum has now been isolated from a variety of different host species including dogs and cattle. Although isolates of this parasite show only minor differences in ultrastructure, considerable differences have been reported in pathogenicity using mainly mouse models. At the DNA level, marked levels of polymorphism between isolates were detected in mini- and microsatellites found in the genome of N. caninum. Knowledge of what drives the biological differences that have been observed between the various isolates at the molecular level is crucial in aiding our understanding of the epidemiology of this parasite and, in turn, the development of efficacious strategies, such as live vaccines, for controlling its impact. The purpose of this review is to document and discuss for the first time, the nature of the diversity found within the species Neospora caninum.

  4. Genetic diversity of caprine Blastocystis from Peninsular Malaysia.

    Science.gov (United States)

    Tan, Tian Chye; Tan, Peng Chiang; Sharma, Reuben; Sugnaseelan, Sumita; Suresh, Kumar Govind

    2013-01-01

    Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9 %) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3 %) followed by ST7 (41.1 %), ST6 (41.1 %), and ST3 (11.0 %) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed.

  5. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    Science.gov (United States)

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.

  6. Human KIR repertoires: shaped by genetic diversity and evolution.

    Science.gov (United States)

    Manser, Angela R; Weinhold, Sandra; Uhrberg, Markus

    2015-09-01

    Killer cell immunoglobulin-like receptors (KIRs) on natural killer (NK) cells are crucially involved in the control of cancer development and virus infection by probing cells for proper expression of HLA class I. The clonally distributed expression of KIRs leads to great combinatorial diversity that develops in the presence of the evolutionary older CD94/NKG2A receptor to create highly stochastic but tolerant repertoires of NK cells. These repertoires are present at birth and are subsequently shaped by an individuals' immunological history toward recognition of self. The single most important factor that shapes functional NK cell repertoires is the genetic diversity of KIR, which is characterized by the presence of group A and B haplotypes with complementary gene content that are present in all human populations. Group A haplotypes constitute the minimal genetic entity that provides high affinity recognition of all major human leukocyte antigen class I-encoded ligands, whereas group B haplotypes contribute to the diversification of NK cell repertoires by providing sets of stimulatory KIR genes that modify NK cell responses. We suggest a cooperative model for the balancing selection of A and B haplotypes, which is driven by the need to provide a suitable corridor of repertoire complexity in which A/A individuals with only 16 different KIR combinations coexist with A/B and B/B donors expressing up to 2048 different clone types.

  7. Genetic diversity in the SIR model of pathogen evolution.

    Science.gov (United States)

    Gordo, Isabel; Gomes, M Gabriela M; Reis, Daniel G; Campos, Paulo R A

    2009-01-01

    We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0)(1+s)) is higher than the fitness of the resident strain (R(0)). We show that this invasion probability is given by the relative increment in R(0) of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  8. Genetic diversity in the SIR model of pathogen evolution.

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    Isabel Gordo

    Full Text Available We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR. We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts, where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0(1+s is higher than the fitness of the resident strain (R(0. We show that this invasion probability is given by the relative increment in R(0 of the new pathogen (s. By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  9. Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

    NARCIS (Netherlands)

    DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common gard

  10. Insight into the Genetic Components of Community Genetics: QTL Mapping of Insect Association in a Fast-Growing Forest Tree

    NARCIS (Netherlands)

    DeWoody, J.; Viger, M.; Lakatos, F.; Tuba, K.; Taylor, G.; Smulders, M.J.M.

    2013-01-01

    Identifying genetic sequences underlying insect associations on forest trees will improve the understanding of community genetics on a broad scale. We tested for genomic regions associated with insects in hybrid poplar using quantitative trait loci (QTL) analyses conducted on data from a common gard

  11. Genetic diversity among five T4-like bacteriophages

    Directory of Open Access Journals (Sweden)

    Bertrand Claire

    2006-05-01

    Full Text Available Abstract Background Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene sequences and genomes. The contribution of the T4-like phages to this overall phage diversity is difficult to assess, since only a few examples of complete genome sequence exist for these phages. Our analysis of five T4-like genomes represents half of the known T4-like genomes in GenBank. Results Here, we have examined in detail the genetic diversity of the genomes of five relatives of bacteriophage T4: the Escherichia coli phages RB43, RB49 and RB69, the Aeromonas salmonicida phage 44RR2.8t (or 44RR and the Aeromonas hydrophila phage Aeh1. Our data define a core set of conserved genes common to these genomes as well as hundreds of additional open reading frames (ORFs that are nonconserved. Although some of these ORFs resemble known genes from bacterial hosts or other phages, most show no significant similarity to any known sequence in the databases. The five genomes analyzed here all have similarities in gene regulation to T4. Sequence motifs resembling T4 early and late consensus promoters were observed in all five genomes. In contrast, only two of these genomes, RB69 and 44RR, showed similarities to T4 middle-mode promoter sequences and to the T4 motA gene product required for their recognition. In addition, we observed that each phage differed in the number and assortment of putative genes encoding host-like metabolic enzymes, tRNA species, and homing endonucleases. Conclusion Our observations suggest that evolution of the T4-like phages has drawn on a highly diverged pool of genes in the microbial world. The T4

  12. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

    Science.gov (United States)

    Rahimi-Mianji, G; Nejati-Javaremi, A; Farhadi, A

    2015-09-01

    The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

  13. Light habitat, structure, diversity and dynamic of the tropical dry forest

    Directory of Open Access Journals (Sweden)

    Omar Melo-Cruz

    2017-01-01

    Full Text Available Tropical dry forests are complex and fragile ecosystems with high anthropic intervention and restricted reproductive cycles. These have unique richness, structural diversity, physiological and phenological . This research was executed  in the Upper Magdalena Valley, in four forest fragments with different successional stages. In each fragment four permanent plots of 0.25 ha were established and lighting habitat associated with richness, relative abundance and rarity of species. The forest dynamics included the mortality, recruitment and diameter growth for a period of 5.25 years. The species rischness found in the mature riparian forestis higher than that reported in other studies of similar areas in Valle del Cauca and the Atlantic coast.  The values of richness, diversity and rarity species are more evidenced  than the magnitudes found in  drier areas of Tolima. The structure, diversity and dynamics of forests were correlated with the lighting habitat, showing differences in canopy architecture and its role in the capture and absorption of radiation. Forests with dense canopy have limited availability of photosynthetically active radiation in understory related low species richness, while illuminated undergrowth are richer and heterogeneous.

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

    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 Fls-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 Tangiiahe 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].

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

    Directory of Open Access Journals (Sweden)

    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].

  16. Parallel responses of species and genetic diversity to El Nino Southern Oscillation-induced environmental destruction

    NARCIS (Netherlands)

    Cleary, D.F.R.; Fauvelot, C.Y.; Genner, J.; Menken, S.B.J.; Mooers, A.O.

    2006-01-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to

  17. Trends over time in tree and seedling phylogenetic diversity indicate regional differences in forest biodiversity change.

    Science.gov (United States)

    Potter, Kevin M; Woodall, Christopher W

    2012-03-01

    Changing climate conditions may impact the short-term ability of forest tree species to regenerate in many locations. In the longer term, tree species may be unable to persist in some locations while they become established in new places. Over both time frames, forest tree biodiversity may change in unexpected ways. Using repeated inventory measurements five years apart from more than 7000 forested plots in the eastern United States, we tested three hypotheses: phylogenetic diversity is substantially different from species richness as a measure of biodiversity; forest communities have undergone recent changes in phylogenetic diversity that differ by size class, region, and seed dispersal strategy; and these patterns are consistent with expected early effects of climate change. Specifically, the magnitude of diversity change across broad regions should be greater among seedlings than in trees, should be associated with latitude and elevation, and should be greater among species with high dispersal capacity. Our analyses demonstrated that phylogenetic diversity and species richness are decoupled at small and medium scales and are imperfectly associated at large scales. This suggests that it is appropriate to apply indicators of biodiversity change based on phylogenetic diversity, which account for evolutionary relationships among species and may better represent community functional diversity. Our results also detected broadscale patterns of forest biodiversity change that are consistent with expected early effects of climate change. First, the statistically significant increase over time in seedling diversity in the South suggests that conditions there have become more favorable for the reproduction and dispersal of a wider variety of species, whereas the significant decrease in northern seedling diversity indicates that northern conditions have become less favorable. Second, we found weak correlations between seedling diversity change and latitude in both zones

  18. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

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    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  19. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Science.gov (United States)

    Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

    2016-01-01

    The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.

  20. Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Donato Matassino

    2014-01-01

    Full Text Available Since 13rd century, Italian domestic autochthonous donkey population has been characterised by Mediterranean grey mousy cruciate ancestral phenotype, currently typical of Amiata donkey (AD genetic type. This phenotype persisted up to the 16th century when a marked introduction of Hispanic and French big sized and dark bay or darkish coloured sires occurred. In the context of a safeguard programme of Latial Equide resources, the aim of this research was to evaluate the genetic diversity and similarity between the AD breed and an autochthonous donkey population native from Lazio, the Viterbese donkey (VD, using molecular markers. A total of 135 animals (50 AD and 85 VD were genetically characterised by using 16 short tandem repeat markers. A high genetic differentiation between populations (FST=0.158; P<0.01 and a low betweenbreeds genetic similarity (0.233±0.085 were observed. Correspondence analysis, the result of STRUCTURE software analysis and analysis of molecular variance would seem to indicate genetically different entities as well. It would be desirable to increase the number of comparison with other breeds to better understand the origin of VD. Moreover, results obtained in this study suggest that the loss of genetic variation observed in VD could mainly derive from unnoticed sub-population structuring (Wahlund effect, rather than to other factors such as inbreeding, null alleles or selection influence.