...combined with small populations, can influence genetic diversity and long-term...mining and energy development. A copper ore smelter, concentrator, and...2007, p. 16). These effects can influence population dynamics,...

Thirty-one occurrences of Erigeron parishii, a narrowly endemic plant threatened by mining, were sampled for allozyme diversity. This taxon held considerable genetic variation at the [4 allozyme loci surveyed. Species (e.g., alleles per locus [A] = 4.3 and proportion of polymorph...

Seabirds endemic to remote oceanic islands face several unique threats to their population viability. Christmas Island is a small oceanic island with remarkable seabird biodiversity, including two endangered endemics: Christmas Island frigatebirds (Fregata andrewsi) and Abbott?s boobies (Papasula abbotti). Christmas Island seabirds are currently threatened by habitat destruction at breeding sites due to phosphate mining and by the adverse effects of the invasive yellow crazy ant (Anoplolepis gracilipes); however, conservation initiatives are limited by a paucity of genetic data on the breeding seabirds. To address this shortcoming, we collected genetic samples from five breeding seabird species, including the two endemics. We surveyed mitochondrial and nuclear genetic diversity, estimated ...

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. We show that the popular core collection assembly procedure ?M? (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Beta vulgaris L. subsp. vulgaris) that is ...

New polymorphic SSR markers in sugarcane has potential usefulness to studies genetic diversity, genetic mapping, DNA fingerprinting and determination offspring as true hybrids, selfing or contaminant in germplasm from breeding program. SSR markers can be obtained in several ways, and the search for SSR-EST sequences an alternative with significant results. The aim of this study was to develop highly polymorphic SSR markers for germplasm studies in sugarcane. Di- tri- and tetra-nucleotide sequences were mined in the TGI bank and 53 EST-SSR markers developed. These markers were analyzed in five genotypes and showed to be highly polymorphic, with the PIC ranging between 0.48 and 0.95 with a mean of 0.86. The discriminatory power ranged from 0.35 to 0.94 with a mean of 0.82 and the genetic sim...

Behavioral studies on genetically diverse mice have proven powerful for determining relationships between phenotypes and have been widely used in alcohol research. Most of these studies rely on naturally occurring genetic polymorphisms among inbred strains and selected lines. Another approach is to introduce variation by engineering single-gene mutations in mice. We have tested 37 different mutant mice and their wild-type controls for a variety (31) of behaviors and have mined this data set by K-means clustering and analysis of correlations. We found a correlation between a stress-related response (activity in a novel environment) and alcohol consumption and preference for saccharin. We confirmed several relationships detected in earlier genetic studies, including positive correlation of a...

Abstract Genetic variation can have important consequences for populations: high population genetic diversity is typically associated with ecological success. Some mechanisms that account for these benefits assume that local social groups with high genetic diversity are more successful than low-diversity groups. At the same time, active decision-making by individuals can influence group genetic diversity. Here, we examine how maternal decisions that determine group genetic diversity influence the viability of Drosophila melanogaster larvae. Our groups contained wild-type larvae, whose genetic diversity we manipulated, and genetically marked -tester- larvae, whose genotype and frequency were identical in all trials. We measured wild-type and tester viability for each group. Surprisingly, th...

Waste deposits produced by metal mining and smelting activities provide extremely difficult habitats for plant colonization and growth. Therefore, plants spontaneously colonizing such areas represent a very interesting system for studying evolution of plant adaptation and population differentiation between contaminated and noncontaminated environments. In this study, two populations of Dianthus carthusianorum, one originating from Zn-Pb waste deposit (a metallicolous population, M) and the other from unpolluted soil (a nonmetallicolous population, NM), were analyzed in respect of their morphological and physiological traits as well as genetic markers. It was found that the plants inhabiting the waste heap differed significantly from the NM plants in terms of leaf size and shape, and these differences were persistent between the first generation of the plants of both populations cultivated under uniform, controlled laboratory conditions. In contrast with the evident morphological differences, no significant differentiation between the populations regarding the physiological traits measured (accumulation of proline, anthocyanins, chlorophyll, carotenoids) was found. These traits can be regarded as neither population specific nor stress markers. The genetic variability was analyzed using 17 random amplified polymorphic DNA (RAPD) and four inter simple sequence repeat (ISSR) markers; this proved that the differentiation between the M and NM populations exists also at the genetic level. Analysis of molecular variance (AMOVA) showed that 24% of the total genetic diversity resided among populations, while 76% - within the populations. However, no significant differences in intrapopulation genetic diversity (Hj) between the M and NM populations of D. carthusianorum was found, which contradicts the theory that acquisition of adaptation mechanisms to adverse, isolated growth habitats is related to reduction in genetic diversity. Distinct genetic differences between the two populations in combination with evident morphological variation support the proposal to regard the M population of D. carthusianorum as a separate calamine ecotype. PMID:23084517

The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. We show that the popular core collection assembly procedure "M" (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Beta vulgaris L. subsp. vulgaris) that is under selection. We present a corrected procedure ("M+") that outperforms M. An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled with M+. A negative correlation in level of allelic diversity between neutral and selected loci was observed in 42% of simulated data sets. When core collection assembly is guided by neutral marker loci, as is the current common practice, enhanced allelic variation at agronomically important loci should not necessarily be expected. PMID:22228243

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers? fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC2F6 progenies, selected from among more than 100 BC2F5 pro...

Humans show tremendous phenotypic diversity across geographically distributed populations, and much of this diversity undoubtedly results from genetic adaptations to different environmental pressures. The availability of genome-wide genetic variation data from densely sampled populations offers unpr...

Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding. PMID:22948437

Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important traits. Despite these challenges, little molecular work has been done to explore genetic diversity and relationships in wild and cultivated black raspberry germplasm. Microsatellite, or simple sequence repeat (SSR), markers are highly polymorphic codominant markers useful for studying genetic diversity, population genetics, genetic fingerprinting and other applications. We examined genetic diversity in 148 wild and cultivated black raspberry accessions using 21 polymorphic SSR markers. Black ras...

The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery. PMID:22736877

Researchers at the National Mine Land Reclamation Center recently received a 450,000 dollar grant from the federal government to clean up the Casselman River watershed in southwestern Pennsylvania. Acid mine drainage has been seepling into the Casselman`s tributaries from underground mining operations, primarily from abandoned deep coal mines in the Shaw mines complex. The restoration plan includes four different technologies: anoxic limestone drains; open limestone drains; diversion wells; and magneto-electrochemical treatment. The principles of these technologies are outlined in the article. 1 fig., 5 photos.

The impact of surface mining for coal on the nature and extent of freshwater wetlands was assessed on 73,200 ha in western Pennsylvania. The influence of mining on wetlands was not uniform across physiographic regions, varying with regional differences in hydrology and soils. Overall, mined lands supported 18% more palustrine wetlands, than unmined lands, primarily because of a 270% gain in permanent, open-water wetlands on mined lands in the glaciated region. Open-water wetlands declined on mined lands in unglaciated regions owing to unfavorable hydrologic conditions. The number and size of emergent wetlands declined as a result of mining. Mined lands supported 81% fewer riverine wetlands than unmined lands. This was caused primarily by avoidance of lands containing streams, and secondarily by a 10% reduction in replacement of riverine wetlands during reclamation. Land managers need to develop land use policies that maximize the ecological and social benefits that can be derived from developing diverse wetland communities on mined lands. 21 references.

Nine microsatellite markers of a widely-distributed seagrass, Thalassia hemprichii, were developed to investigate genetic diversity and genetic connectivity. The number of alleles detected per locus ranged from 3 to 26, and the expected and observed heterozygosities ranged from 0.00 to 1.00 and 0.00 to 0.87, respectively. The markers described here are sufficiently polymorphic and informative to investigate the genetic diversity, genetic connectivity and genetic structure of T. hemprichii.

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed. PMID:22837830

ABSTRACT: BACKGROUND: Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. RESULTS: A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B - genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A - and B - genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. CONCLUSIONS: Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut. PMID:23140574

Successful recovery and sustainability of threatened and exploited species depends in part on retention and maintenance of genetic diversity. Theory indicates that genetic diversity is lost at a rate inversely proportional to the genetically effective population size (Ne), which is roughly equal to ...

Abstract Recent research in community genetics has examined the effects of intraspecific genetic variation on species diversity in local communities. However, communities can be structured by a combination of both local and regional processes and to date, few community genetics studies have examined whether the effects of instraspecific genetic variation are consistent across levels of diversity. In this study, we ask whether host-plant genetic variation structures communities of arthropod inquilines within distinct habitat patches - rosette leaf galls on tall goldenrod (Solidago altissima). We found that genetic variation determined inquiline diversity at both local and regional spatial scales, but that trophic-level responses varied independently of one another. This result suggests that...

A total of 360 Rhizobium leguminosarum bv. viciae strains was isolated from three brown-coal mining restoration fields of different age and plant cover (without and in the first and second year of alfalfa, Medicago sativa, cultivation) using two host species (Vicia hirsuta and Pisum sativum) as capture plants. The strains were genetically typed by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-generated 16S-23S ribosomal DNA intergenic spacer regions (IGS-RFLP) and characterized by plasmid profiles and RFLP analysis of amplified nodABC genes. The R. leguminosarum bv. viciae population was dominated by the same group of strains (irrespective of the trap plant used). According to type richness, the genetic diversity of indigenous R. leguminosarum in the second year of restoration was lower than in the first year and it resembled that of the fallow field, except for plasmid types, in which it was higher than that of the fallow field. Some of the less frequent nodABC genotypes were associated with distinct chromosomal IGS genotypes and symbiotic plasmids (pSyms) of different sizes, indicating that horizontal transfer and rearrangements of pSym can occur in natural environments. However, the dominant pSym and chromosomal genotypes were strictly correlated suggesting a genetically stable persistence of the prevailing R. leguminosarum bv, viciae genotypes in the absence of its host plant.

The North Central Regional Plant Introduction Station (NCRPIS) located in Ames, Iowa maintains a large collection of diverse plant germplasm. Controlled pollination of individual accessions is necessary to preserve the original genetic diversity. Some plants, especially those with conspicuous flowe...

Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encode nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from sunflower (Helianthus annuus L.), and most of the previously identified homologs are members of two large NBS-LRR clusters harboring downy mildew R-genes. We mined the sunflower EST database and used comparative genomics approaches to develop a deeper understanding of the diversity and distribution of NBS-LRR homologs in the sunflower genome. Collectively, 630 NBS-LRR homologs were identified, 88 by mining a database of 284,241 sunflower ESTs and 542 by sequencing 1,248 genomic DNA amplicons isolated from common and wild sunflower species. DNA markers were developed from 196 unique NBS-LRR sequences and facilitated genetic mapping of 167 NBS-LRR loci. The latter were distributed throughout the sunflower genome in 44 clusters or singletons. Wild species ESTs were a particularly rich source of novel NBS-LRR homologs, many of which were tightly linked to previously mapped downy mildew, rust, and broomrape R-genes. The DNA sequence and mapping resources described here should facilitate the discovery and isolation of recognition-dependent R-genes guarding sunflower from a broad spectrum of economically important diseases. Sunflower nucleotide and amino acid sequences have been deposited in DDBJ/EMBL/GenBank under accession numbers EF 560168-EF 559378 and ABQ 58077-ABQ 57529. PMID:18553106

... - Davis; Maria S Sanchez; Bioinformatic Analysis of the Effects of Genetic and Spatial Diversity on ... Protein Structures Using Geometric Morphometric Methods: An Assessment of Structural Similarity ...

A review of genomics research is presented for the three most economically important palm crops, coconut (Cocos nucifera), date palm (Phoenix dactylifera) and oil palm (Elaeis guineensis), encompassing molecular markers studies of genetic diversity, genetic mapping, quantitative trait loci discovery...

Increasingly, lands intended for mining, or lands that have been mined and reclaimed, are being evaluated in terms of biological diversity (biodiversity). The concept of biodiversity includes die variety and number of living organisms, their organizations, and the environments that support them. This paper presents a framework for discussing and evaluating biodiversity and for constructing checklists for evaluating biodiversity before and after mining. This framework identifies some of the different types of biodiversity applicable to mineral lands, die ranges of scale at which they are applicable, and the social stakes and stakeholders relevant across scale and diversity types.

Data Mining, also known as Knowledge Discovery in Databases, is a process used to extract implicit, previously unknown, but potentially useful information from raw data. This first website (1) provides a basic overview of Data Mining and some applications for the process. Common applications of data mining include fraud detection and marketing, but data mining has also been applied in paleoecology, and medical genetics as described on this website from the University of Helsinki (2). This website from the University of Massachusetts, Amherst (3) describes a project involving the development of new algorithms that will be applied to the creation of two large-scale databases to be used to "enable insight into government efficiency and the flow of scientific ideas." This white paper (4) provides a nice educational resource for Data Mining. If you are inspired to try your the process, the Weka Machine Learning Project from Waikato University (5) offers open source software that can be used for data mining tasks. KD Nuggets (6) posts articles on Data Mining, Knowledge Discovery, Genomic Mining, Web Mining that range from the serious to the silly, along with other resources. For a brief history of data mining and related fields, visit this website (7). Finally, The Data Mine website (8) is an excellent place to venture into further explorations on Data Mining.

An introduction to statistical data mining, Data Analysis and Data Mining is both textbook and professional resource. Assuming only a basic knowledge of statistical reasoning, it presents core concepts in data mining and exploratory statistical models to students and professional statisticians-both those working in communications and those working in a technological or scientific capacity-who have a limited knowledge of data mining.This book presents key statistical concepts by way of case studies, giving readers the benefit of learning from real problems and real data. Aided by a diverse rang

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands, and the United States to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active male HF populations in each country by using pedigree data. Measures of genetic diversity such as probability of gene origin inbreeding and kinship were calculated. The cryobanks have captured substantial amounts of genetic diversity for the HF compared with the current populations. A substantial part of the US, French, and Dutch collections seems to be genetically similar. On the other hand, the US collection in particular represents an interesting reservoir of HF genes of the past. Gene banks can play an important role in conserving genetic diversity within livestock breeds over time, and may support industry in the future when needed. PMID:21787945

The diversity of the largest group of plant disease resistance genes, the nucleotide binding site-leucine-rich repeat (NBS-LRR) genes, was examined in cereals following polymerase chain reaction (PCR) cloning and database mining. NBS-LRR genes in rice are a large and diverse class with more than 600...

Commercial applications of data mining in areas such as e-commerce, market-basket analysis, text-mining, and web-mining have taken on a central focus in the JCDD community. However, there is a significant amount of innovative data mining work taking place in the context of scientific and engineering applications that is not well represented in the mainstream KDD conferences. For example, scientific data mining techniques are being developed and applied to diverse fields such as remote sensing, physics, chemistry, biology, astronomy, structural mechanics, computational fluid dynamics etc. In these areas, data mining frequently complements and enhances existing analysis methods based on statistics, exploratory data analysis, and domain-specific approaches. On the surface, it may appear that data from one scientific field, say genomics, is very different from another field, such as physics. However, despite their diversity, there is much that is common across the mining of scientific and engineering data. For example, techniques used to identify objects in images are very similar, regardless of whether the images came from a remote sensing application, a physics experiment, an astronomy observation, or a medical study. Further, with data mining being applied to new types of data, such as mesh data from scientific simulations, there is the opportunity to apply and extend data mining to new scientific domains. This one-day workshop brings together data miners analyzing science data and scientists from diverse fields to share their experiences, learn how techniques developed in one field can be applied in another, and better understand some of the newer techniques being developed in the KDD community. This is the fourth workshop on the topic of Mining Scientific Data sets; for information on earlier workshops, see http://www.ahpcrc.org/conferences/. This workshop continues the tradition of addressing challenging problems in a field where the diversity of applications is matched only by the opportunities that await a practitioner.

Recent research in community genetics has examined the effects of intraspecific genetic variation on species diversity in local communities. However, communities can be structured by a combination of both local and regional processes and to date, few community genetics studies have examined whether the effects of instraspecific genetic variation are consistent across levels of diversity. In this study, we ask whether host-plant genetic variation structures communities of arthropod inquilines within distinct habitat patches--rosette leaf galls on tall goldenrod (Solidago altissima). We found that genetic variation determined inquiline diversity at both local and regional spatial scales, but that trophic-level responses varied independently of one another. This result suggests that herbivores and predators likely respond to heritable plant traits at different spatial scales. Together, our results show that incorporating spatial scale is essential for predicting the effects of genetically variable traits on different trophic levels and levels of diversity within the communities that depend on host plants. PMID:19243408

One should perhaps start off by asking the question, 'But what wood is it we want to see?' There are so many trees that make up the wood; within a post-genomics context, genes, transcripts, proteins, and metabolites are the more tangible ones. Rather than studying these components in isolation, a more holistic approach is to unravel the interactions between the myriad of subcellular components and this is vital to systems biology. Moreover, this will help define the phenotype of the organism under investigation. Metabolomics is complementary to transcriptomics and proteomics, and despite the immense metabolite diversity observed in plants, metabolomics has been embraced by the plant community and in particular for studying metabolic networks. Whilst post-genomic science is producing vast data torrents, it is well known that data do not equal knowledge and so the extraction of the most meaningful parts of these data is key to the generation of useful new knowledge. A metabolomics experiment is guaranteed to generate thousands of data points (e.g. samples multiplied by the levels of particular metabolites) of which only a handful might be needed to describe the problem adequately. Evolutionary computational-based methods such as genetic algorithms and genetic programming are ideal strategies for mining such high-dimensional data to generate useful relationships, rules, and predictions. This article describes these techniques and highlights their usefulness within metabolomics. PMID:15596480

Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.uiuc.edu/), a system of open-air rings within which [CO(2)] is elevated to approximately 550 ppm. Data from multiple rings, comparing plants in ambient air and elevated [CO(2)], were analyzed by mixed model ANOVA, linear discriminant analysis (LDA) and data-mining tools. In elevated [CO(2)], decreases in the expression of genes related to chloroplast functions characterized all lines but individual members of distinct multi-gene families were regulated differently between lines. Also, different strategies distinguished the lines with respect to the regulation of genes related to carbohydrate biosynthesis and partitioning, N-allocation and amino acid metabolism, cell wall biosynthesis, and hormone responses, irrespective of the plants' developmental status. Metabolite results paralleled reactions seen at the level of transcript expression. Evolutionary adaptation of species to their habitat and intrinsic genetic plasticity seem to determine the nature of responses to elevated [CO(2)]. Irrespective of their underlying genetic diversity, and evolutionary adaptation to different habitats, a small number of common, predominantly stress-responsive, signature transcripts appear to characterize responses of the Arabidopsis ecotypes in FACE. PMID:16941220

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island popu...

The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European ...

Genetic diversity can benefit social insects by providing variability in immune defences against parasites and pathogens. However, social parasites of ants infest colonies and not individuals, and for them a different relationship between genetic diversity and resistance may exist. Here, we investig...

Roads exert various effects of conservation concern. They cause road mortality of wildlife, change the behaviour of animals and lead to habitat fragmentation. Roads also have genetic effects, as they restrict animal movement and increase the functional isolation of populations. We first formulate theoretical expectations on the genetic effects of roads with respect to a decrease in genetic diversity and an increase in genetic differentiation or distance of populations or individuals. We then review the empirical evidence on the genetic effects of roads based on the available literature. We found that roads often, but not always, decrease the genetic diversity of affected populations due to reduced population size and genetic drift. Whether the reduction in genetic diversity influences the ...

Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. PMID:22369278

The effect of aquaculture effluent on community structure was examined in a stream formed by the discharge of treated acid mine water. The mine water stream and the raceway stream whose source was treated mine water were sampled. In addition, a site below the confluence of the mine water and raceway streams was also sampled. Initially, there were no significant differences in macroinvertebrate density, diversity or community structure in the closed canopy, low light, mine water and raceway streams. However, in the high light environment below the confluence, the community included a substantial proportion of grazers and density was significantly lower. After an inadvertent resuspension of precipitated metal hydroxides from the AMD treatment facility, communities in the mine water stream and below the confluence were strongly dominated by chironomids while the raceway stream maintained much of its diversity. At the end of the study period diversity in all streams was significantly greater than in earlier samples however, densities were 6-8x lower than initial values in the raceway and mine water streams. This study demonstrated that there was little effect of aquaculture effluent on the benthic community in a low-light environment. Additionally, aquaculture effluent mediated the negative effects of AMD metals.

We review previous studies on the genetic diversity of malaria vectors to highlight the major trends in population structure and demographic history. In doing so, we outline key information about molecular markers, sampling strategies and approaches to investigate the causes of genetic structure in Anopheles mosquitoes. Restricted gene flow due to isolation by distance and physical barriers to dispersal may explain the spatial pattern of current genetic diversity in some Anopheles species. Nonetheless, there is noteworthy disagreement among studies, perhaps due to variation in sampling methodologies, choice of molecular markers, and/or analytical approaches. More refined genealogical methods of population analysis allowing for the inclusion of the temporal component of genetic diversity fa...

When raw material is extracted from multiple mines or faces and when the construction of a mine facility is being planned, the selection for the optimal location of the facility is an important consideration because of high transportation costs. This paper presents an approach for the selection of optimal location of a mining facility based on the genetic algorithms which is a directed random search technique. The technique, simple and easy to apply, is demonstrated for the case of the location of a coal washery plant, whose supply comes from five mines with varying reserves and coal qualities, topographical conditions and mine status. The result shows that the solution produced by the proposed algorithm can be used to find the optimal location of any mining facility.

Global changes currently result in strong declines in species richness and population-genetic diversity. For maintenance of diversity in protected areas and developing new diversity in restored or newly created areas, immigration by long-distance dispersal (LDD) is of vital importance, as it allows ...

The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders. PMID:22466957

• Premise of the study: Average arctic temperatures have increased at almost twice the global average in the past 100 years. Most studies on biodiversity along latitudinal gradients have focused on species richness or genetic diversity at lower latitudes, and only a few studies have inferred genetic diversity within a species along a latitudinal gradient at higher latitudes, even though these areas might be most affected by recent climate changes. Here, intraspecific genetic diversity of the arctic-alpine Dryas octopetala (Rosaceae) is studied along a latitudinal gradient to test the hypotheses that genetic diversity decreases and vegetative clonal growth increases with latitude. • Methods: Ten microsatellite markers have been developed for D. octopetala and analyzed with population genetic methods in five populations along a latitudinal transect spanning from 59.0°N to 79.9°N. • Key results: The nine microsatellites that were used in the final analyses resulted in a resolution high enough to distinguish between ramets while providing useful information at a larger geographical scale. Three genetic clusters were indicated, a southern Norway group, a northern Norway group, and a Svalbard group, with corresponding decreasing genetic diversity. No trend was found with regard to clonality along the gradient. • Conclusions: The newly developed microsatellite markers provide a useful tool for further genetic studies of D. octopetala and its close relatives, addressing population structure as well as phylogeographic patterns. The results of this study support the hypothesis of decreasing genetic diversity with increasing latitude, which may have implications for future adaptability to climate change. PMID:21622468

Terminalia trees are being over-exploited because of their medicinal and economical importance leading to loss of valuable genetic resources. For sustainable utilization and conservation, assessment of genetic diversity therefore becomes imperative. We report a comprehensive first study on estimation and analysis of genetic variation through Amplified fragment length polymorphism (AFLP), inter simple sequence repeat polymorphism (ISSR) and random amplification of polymorphic DNA (RAPD) across three species of Terminalia. The study included (i) characterization of genetic diversity at interspecific level, and (ii) comparison of efficiency of the marker systems. That the three species are genetically distinct was revealed by all the three marker systems as unique DNA fingerprints were obtain...

Population fragmentation is often correlated with loss of genetic diversity and reduced fitness. Obligate out-crossing (dioecy) is expected to enhance genetic diversity, reduce genetic differentiation, and avoid inbreeding depression through frequent gene flow. However, in highly fragmented populations dioecy has only diminishing effects upon genetic structure as pollination limitations (e.g. flight distance of pollinators) most often restrict inter-population gene flow in insect pollinated species. In fragmented dry grasslands in northeastern Germany, we analysed genetic structure, fitness, and habitat quality of the endangered dioecious Silene otites (Caryophyllaceae). Using AFLP markers, a high level of differentiation among ten populations was found (F st = 0.36), while the intra-pop...

Plant genetic resources (PGR) for food and agriculture (PGRFA) are vital components of biodiversity. They meet human needs for food, fiber, shelter, and medicines, and contribute to trade and cultural traditions. They form building blocks for the adaptation, evolution, and survival of species and for crop improvement programs that support sustainable development. PGR loss is occurring at an alarming rate, and threatens global food security by decreasing the ability of crops to adapt to environmental and biotic challenges. Here, I discuss the causes of this genetic erosion. Crop genetic diversity must be conserved and used sustainably to ensure sustainable development. We must also train a critical mass of scientists to manage this resource, undertake research to increase utilization of PGRFA, and develop policies and legislation to guide their conservation and utilization. Conservation via ex situ or in situ strategies can guarantee the availability of PGRFA for present and future generations. Conservation through sustainable utilization promotes long-term conservation of these resources. Education and training in PGR conservation and management are important to increase the critical mass of trained staff on all aspects of PGR conservation and management. Post-graduate degrees in PGRFA conservation and management are now offered by the Philippines, India, and Malaysia to meet the regional need for trained staff. In addition, short-term training for stakeholders is provided by governments and nongovernmental organizations. Research on “allele mining”, especially to detect genes for adaptation to climate change and emerging pests and diseases, is necessary to increase the utilization of conserved germplasm, determine the scientific underpinnings of on-farm conservation, and develop the potential to identify and utilize novel products. Awareness of national and international policies and laws on biodiversity conservation and PGRFA must also be increased to improve the conservation and sustainable utilization of PGRFA.   

Knowledge of genetic diversity and relationships among Beta vulgaris genetic resources is essential for their conservation and development of breeding populations. In this study, we compared patterns of genetic variability and quantitative morphological data between a sea and a ruderal beet populati...

We used a comparative approach to investigate the impact of the disposal of gold mine tailings into the ocean near the Lihir mine (Niolam Island, Papua New Guinea). We found abundance and diversity of zooplankton, micronekton and pelagic fish to be similar or higher in the mine region compared to the reference site. We also found relatively high trace metal concentrations in lower trophic level groups, especially zooplankton, near the mine discharge, but few differences in tissue concentrations of micronekton, baitfish and pelagic fish between the two regions. Biomagnification of some trace metals by micronekton, and of mercury by fish was evident in both regions. We conclude that ocean mine waste disposal at Niolam Island has a local impact on the smaller and less mobile pelagic communities in terms of trace metal concentrations, but has little effect on the abundance and biodiversity of the local food web. PMID:23079701

Seasonal changes in genetic diversity of Meriones meridianus and Dipus sagitta populations in the Ningxia Hui Autonomous Region were monitored using inter-simple sequence repeats. There were 45 discernible DNA fragments isolated from 33 samples of M. meridianus, and 25 from 40 samples of D. sagitta. The differences in gene frequencies are statistically significant for some alleles. Nei?s index revealed that the greatest genetic differentiation was distributed within the seasonal groups. Nei?s and Shannon?s indexes exhibited similar seasonal trends, indicating that the spring group has the highest level of genetic diversity and that genetic diversity changes with the seasons. Correlation analysis found no statistically significant correlation between genetic diversity and population density...

As key 'ecosystem engineers', earthworms improve mineralization of organic matter, plant growth, soil quality, and are an important component of many terrestrial food webs. Under appropriate conditions, they are therefore likely to accelerate the restoration of soil ecosystem function after mining. Conserving naturally occurring populations and facilitating their recolonisation appears as the most efficient way to increase earthworms' overall effect. The impact of mining activities and restoration measures on New Zealand endemic earthworm communities was tested. Earthworm biomass and diversity were compared in four different habitat types. Mining activities, not surprisingly, are shown here to have a detrimental impact on earthworm communities. Soil stockpiling induces anaerobic conditions...

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

Topics covered include drilling and blasting, mine haulage, mining equipment, mine automation, surface mining, coal mining, strata control, ventilation, mine design and planning, coal preparation and ore processing.

Successful colonization and/or invasion depend on characteristics of the invaded community and of the colonizer itself. Although many studies have documented a negative relationship between invasibility and biodiversity, the importance of community evenness is rarely examined and thus poorly understood. However, colonizer characteristics, including population genetic diversity, can also be important determinants of colonization success. We conducted a greenhouse experiment to assess the relative importance of community evenness and colonizer population genetic diversity using the weed Arabidopsis thaliana. We added seeds of A. thaliana (varying genetic diversity while keeping propagule pressure constant) to four types of constructed plant communities: those dominated by legumes, grasses or...

Abstract The importance of species diversity to emergent, ecological properties of communities is increasingly appreciated, but the importance of within-species genetic diversity for analogous emergent properties of populations is only just becoming apparent. Here, the properties and effects of genetic variation on predation resistance in populations were assessed and the molecular mechanism underlying these emergent effects was investigated. Using biofilms of the ubiquitous bacterium Serratia marcescens, we tested the importance of genetic diversity in defending biofilms against protozoan grazing, a main source of mortality for bacteria in all natural ecosystems. S.marcescens biofilms established from wild-type cells produce heritable, stable variants, which when experimentally combined, ...

Common applications of data mining include fraud detection and marketing, but data mining has also been applied in paleoecology, and medical genetics as described on this website from the University of Helsinki. The project "develops methods and tools for analyzing large data sets and for searching for unexpected relationships in the data." They are also applying their research to text analysis to automatically create a summary of a document and locate related news items from feeds.

Genetic diversity and reproductive mode can control whether an introduced species becomes invasive. Here we use genetic tools to compare the non-native, invasive Phragmites australis to its native conspecific, P. australis subsp. americanus, in wetlands of Utah and southern Idaho. We found striking differences in genetic structuring, population diversity, and mode of reproduction between the two lineages. Non-native P. australis exhibited substantially more genetic homogeneity among populations, greater local genet richness, greater genetic diversity among individuals, and smaller average clone size compared to the native lineage. These findings suggest that non-native P. australis relies more heavily on sexual reproduction and disperses pollen and/or seeds more widely than native P. austr...

Jackfruit ( Artocarpus heterophyllus Lam.) Diversity in Bangladesh: Land Use and Artificial Selection. Bangladesh is often recognized as a secondary center of diversity for jackfruit (Artocarpus heterophyllus Lam.) and is expected to harbor important genetic diversity of this underutilized tree crop. Unfortunately, genetic erosion is occurring before this rich local resource has been documented and utilized for potential crop improvement. The aim of this study was to carry out a village-based survey and make morphological measurements to document and assess jackfruit diversity across trees associated with a gradient of three locations/habitats (homesteads, public lands, and forest or fallow lands). We also tested the hypotheses that cultivated jackfruit found in homesteads exhibited positi...

We propose a new method of design called MORDE (multi-objective robust design exploration) that combines a multi-objective robust optimization approach and data-mining techniques for analyzing trade-offs. The probabilistic representation of design parameters, which is compatible with the Taguchi method, is incorporated into the optimization system we previously developed that uses a multi-objective genetic algorithm. The means and standard deviations of responses of evaluation functions against uncertainties in design variables are evaluated by descriptive Latin hypercube sampling using Kriging surrogate models. Design space is visualized by Self-organizing map (SOM). To extract design rules further, a new approach that adopts the association rule with an "aspiration vector" is proposed. MORDE is then applied to an industrial design problem with a centrifugal fan for a washer-dryer. Taking dimensional uncertainty into account, we optimize the means and standard deviations of the resulting distributions of the fan efficiency and turbulent noise level. Steady Reynolds-averaged Navier Stokes simulations are carried out to collect the necessary dataset for Kriging models. We demonstrate the advantages of the proposed method of multi-objective robust optimization over traditional non-robust ones in that the solutions are diverse. We clarify that the association rule can extract both sufficient and necessary conditions as design rules to achieve trade-off balances. The association rule is also more beneficial than SOM in finding quantitative relations, particularly those that are concerned with more than three design parameters.

Background Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway. Results In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing. Conclusion While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize

Setaria italica and its wild ancestor Setaria viridis are diploid C(4) grasses with small genomes of ?515 Mb. Both species have attributes that make them attractive as model systems. Setaria italica is a grain crop widely grown in Northern China and India that is closely related to the major food and feed crops maize and sorghum. A large collection of S. italica accessions are available and thus opportunities exist for association mapping and allele mining for novel variants that will have direct application in agriculture. Setaria viridis is the weedy relative of S. italica with many attributes suitable for genetic analyses including a small stature, rapid life cycle, and prolific seed production. Setaria sp. are morphologically similar to most of the Panicoideae grasses, including major biofuel feedstocks, switchgrass (Panicum virgatum) and Miscanthus (Miscanthus giganteus). They are broadly distributed geographically and occupy diverse ecological niches. The cross-compatibility of S. italica and S. viridis also suggests that gene flow is likely between wild and domesticated accessions. In addition to serving as excellent models for C(4) photosynthesis, these grasses provide novel opportunities to study abiotic stress tolerance and as models for bioenergy feedstocks. PMID:21459768

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Mosses and other bryophytes are vital components of forests, because they sustain a tremendous diversity of invertebrates and influence significant ecological functions. There have been few studies on moss population diversity in Southeast Asia, despite the escalating deforestation in this region of rich biodiversity. The genetic diversity of the tropical moss Acanthorrhynchium papillatum (Harv.) Fleisch., collected from forested areas in Singapore and Peninsular Malaysia, was elucidated using eight microsatellite markers developed for this species. Significant levels of allelic and haplotypic diversity were observed among clumps of the moss. Differences in allelic richness and genotypic diversity among the populations were higher in less disturbed forests compared to the more disturbed areas, suggesting that genetic diversity is affected by habitat quality. Genetic diversity levels within the clumps studied were low, indicating that vegetative reproduction was more important within clumps than sexual reproduction. However, multilocus genotypes of samples within the clumps studied were not all alike, providing evidence of microsatellite mutation or of occasional sexuality. Despite the isolation of populations, A. papillatum can introduce genetic variability by mutation among vegetatively propagated individuals. This study provides baseline information on the genetic diversity of A. papillatum tropical rain forests. PMID:22882300

Marginal populations are often geographically isolated, smaller, and more fragmented than central populations and may frequently have to face suboptimal local environmental conditions. Persistence of these populations frequently involves the development of adaptive traits at phenotypic and genetic levels. We compared population structure and demographic variables in two fucoid macroalgal species contrasting in patterns of genetic diversity and phenotypic plasticity at their southern distribution limit with a more central location. Models were Ascophyllum nodosum (L.) Le Jol. (whose extreme longevity and generation overlap may buffer genetic loss by drift) and Fucus serratus L. (with low genetic diversity at southern margins). At edge locations, both species exhibited trends in life-history...

Humans have played a significant role in reducing levels of genetic diversity and differentiation of many teleost fishes, leading to homogenization across biological entities. We compare patterns of historical and contemporary genetic structure for three sympatric Great Lake?s lake trout (Salvelinus namaycush) morphs (lean, siscowet, and humper) that differ in patterns of habitat occupancy, susceptibility to overfishing and predation by invasive sea lamprey (Petromyzon marinus). Differential susceptibilities to overfishing and predation were expected to result in different impacts to levels of genetic diversity loss for each morphotype. Genetic data was collected for samples at three points in time: 1948 (pre-collapse), 1959 (collapse) and 1990s (current), corresponding to periods of inten...

Empirical data on genetic counseling outcomes in the deaf population are needed to better serve this population. This study was an examination of genetics knowledge before and after culturally and linguistically appropriate pre-test genetic counseling in a diverse deaf adult sample. Individuals ?18?years old with early-onset sensorineural deafness were offered connexin-26/30 testing and genetic counseling. Participants completed questionnaires containing 10 genetics knowledge items at baseline and following pre-test genetic counseling. The effects of genetic counseling, prior beliefs about etiology, and participant?s preferred language on genetics knowledge scores were assessed (n?=?244). Pre-test genetic counseling (p?=?.0007), language (p?p?p?=?.035) were predictors of genetics knowledge...

Surface coal mining with valley fills has impaired the aquatic life in numerous streams in the Central Appalachian Mountains. We characterized macroinvertebrate communities from riffles in 37 small West Virginia streams (10 unmined and 27 mined sites with valley fills) sampled in the spring index period (March-May) and compared the assessment results using family- and genus-level taxonomic data. Specific conductance was used to categorize levels of mining disturbance in mined watersheds as low (<500 {mu} S/cm), medium (500-1000 {mu} S/cm), or high (>1000 {mu} S/cm). Four lines of evidence indicate that mining activities impair biological condition of streams: shift in species assemblages, loss of Epherneroptera taxa, changes in individual metrics and indices, and differences in water chemistry. Results were consistent whether family- or genus-level data were used. In both family- and genus-level nonmetric multidimensional scaling (NMS) ordinations, mined sites were significantly separated from unmined sites, indicating that shifts in community structure were caused by mining. Several Epherneroptera genera (e.g., Ephemerella, Epeorus, Drunella) and their families (Ephemerellidae, Heptageniidae) were correlated most strongly with the primary NMS axis. These same Ephemeroptera were absent and, thus, eliminated from most of the mined sites. Total Ephemeroptera richness and relative abundance both declined with increasing mining disturbance. Several other metrics, such as richness, composition, tolerance, and diversity, clearly discriminated unmined vs mined sites. The results show that mining activity has had subtle to severe impacts on benthic macroinvertebrate communities and that the biological condition most strongly correlates with a gradient of ionic strength.

The Common Wall Lizard (Podarcis muralis) has established more than 150 non-native populations in Central Europe, stemming from eight geographically distinct evolutionary lineages. While the majority of these introduced populations are found outside the native range, some of these populations also exist at the northern range margin in southwestern Germany. To (i) infer the level of hybridization in contact zones of alien and native lineages; and (ii) compare the genetic diversity among purebred introduced, native and hybrid populations, we used a combination of maternally inherited markers (mtDNA: cytb) and Mendelian markers (microsatellites). Our results suggest a rapid genetic assimilation of native populations by strong introgression from introduced lineages. Discordant patterns of mtDNA and nDNA variation within hybrid populations may be explained by directed mate choice of females towards males of alien lineages. In contrast to previous studies, we found a nonlinear relationship between genetic diversity and admixture level. The genetic diversity of hybrid populations was substantially higher than in introduced and native populations belonging to a single lineage, but rapidly reaching a plateau of high genetic diversity at an admixture level of two. However, even introduced populations with low founder sizes and from one source population retained moderate levels of genetic diversity and no evidence for a genetic bottleneck was found. The extent of introgression and the dominance of alien haplotypes in mixed populations indicate that introductions of non-native lineages represent a serious threat to the genetic integrity of native populations due to the rapid creation of hybrid swarms. PMID:22765844

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. PMID:22535388

Oct 4, 2006... have led to very high levels of genetic diversity and phenotypic variation. ... Popular Science claims that "worms, planets, and extra dimensions" are just ... regardless of race, sex, age, religion, color, national origin, ancestry, ...

Keywords: Agro-biodiversity, farmer varieties, indigenous knowledge, farmer-participatory research, genetic diversity, genotype-by-environment interaction, germplasm collection, Ipomoea batatas , specific adaptation, yield stability, sweetpotato, variance component estimates.

Plants recognize microbes via specific pattern recognition receptors that are activated by microbe-associated molecular patterns (MAMPs), resulting in MAMP-triggered immunity (MTI). Successful pathogens bypass MTI in genetically diverse hosts via deployment of effectors (virulence factors) that inhi...

... motion (“Lagrangian” grid) can prevent numerical dispersion during wave- induced vertical transport. ... The driving force for isopycnal model develop-ment is genetic diversity. ... The choice of reference profile affects the modeled circulation.

Abstract Akt/PKB serine/threonine kinase is a leading signalling modulator for several cellular processes including metabolism, growth, proliferation and survival. However, complexity and diversity in the upstream/downstream arms of Akt pathway, as recent genetic studies reported, challenge ...

Among different teleost fish species, diverse sex-determining mechanisms exist, including environmental and genetic sex determination, yet chromosomal sex determination with male heterogamety (XY) prevails. Different pairs of autosomes have evolved as sex chromosomes among species in the same genus ...

Genetic diversity (?), effective population size (Ne), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history o...

Coniothyrium canker caused by the fungal pathogen Teratosphaeria (= Coniothyrium) zuluensis is one of the most important diseases affecting plantation-grown Eucalyptus trees. Little is known regarding the pathogen and this study consequently considers the genetic diversity and population structure o...

Whole genome sequencing projects have produced draft sequences for species from diverse evolutionary clades for comparative evolutionary studies. Generally, these projects have not simultaneously created extensive single nucleotide polymorphism (SNP) resources for use in genetics studies within the...

Genetic diversity among Sodalis glossinidius populations was investigated using amplified fragment length polymorphism markers. Strains collected from Glossina palpalis gambiensis and Glossina morsitans morsitans flies group into separate clusters, being differentially structured. This differential ...

Poaching and habitat destruction across sub-Saharan Africa brought the black rhinoceros (Diceros bicornis) close to extinction. Over the past few decades, however, one of four subspecies, D. b. bicornis, has experienced a significant population increase as a consequence of its protection within Etosha National Park (ENP), Namibia. We report here on the level and spatial distribution of black rhinoceros genetic diversity within ENP. Using nine microsatellite loci, genetic variation was assessed from 144 individuals. Our results are consistent with the observation of lower levels of genetic diversity in D. b. bicornis, when compared to D. b. michaeli, but greater diversity when compared to D. b. minor. We also showed that ENP?s black rhino genetic diversity is well represented in Waterberg N...

Amplified fragment length polymorphism (AFLP) was used to analyze the genetic diversity and variation of two populations of Pleuronectes yokohamae from China and North Korea. A total of 228 loci ranging in size were detected from 63 individuals, of which 139 were polymorphic. The number of bands per primer combination varied from 37 to 51 and the percentage of polymorphic bands per primer combination ranged from 43.14% to 72.97%. The proportion of polymorphic loci, the Nei's genetic diversity and Shannon genetic diversity index of China and North Korea populations were 55.09% and 55.71%, 0.1205 and 0.1917, 0.1370 and 0.2129, respectively. The results showed that the genetic diversity of these two populations was at the same level. Dominant gene frequency revealed that these two populations...

Natural Saccharomyces cerevisiae yeast strains exhibit very large genotypic and phenotypic diversity. However, the link between phenotype variation and genetic determinism is still difficult to identify, especially in wild populations. Using genome hybridization on DNA microarrays, it is now possibl...

Genetic diversity analyses of tropical tree species are relevant to landscape management, plant genetic resource inventory, and biological conservation of threatened species. Annona crassiflora is an endangered fruit tree native to the Cerrado biome that is threatened by reduction of natural populations and fruit extraction. We examined the intra- and interpopulational genetic diversity of this species in the northern region of Minas Gerais State. Seventy-two individuals from four natural populations were genotyped using RAPD markers. We found moderate genetic diversity among populations, with Shannon's I index varying between 0.31 and 0.44, and Nei's genetic diversity (H(E)) for the population set equal to 0.31. AMOVA indicated a greater genetic variation within (77.38%) rather than among populations (22.62%), tending towards isolation by distance (Mantel's r = 0.914; P = 0.089). Nei's genetic identity estimates among populations revealed a hierarchical pattern of genetic similarity of form [(CA1, CA2), MC], [(GM)], corroborating the high genetic differentiation between spatially isolated populations. PMID:21968724

This volume shows how the cooperation of geochemists and groundwater geologists provides our current theoretical bases of chemical hydrogeology. Vital information helps one understand and cope with diverse problems such as management of radioactive and toxic wastes, development of water supplies, formation of ore deposits, and hydrologic effects of mining and oil production.

MOTIVATION: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTM...

The conformational diversity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational diversity of the phosphate group of ATP obtained computationally.

The southeastern United States and Florida support an unusually large number of endemic plant species, many of which are threatened by anthropogenic habitat disturbance. As conservation measures are undertaken and recovery plans designed, a factor that must be taken into consideration is the genetic composition of the species of concern. Here we describe the levels, and partitioning, of genetic diversity in 17 populations of the rare and threatened Florida endemic, Euphorbia telephioides (telephus spurge). Species-wide genetic diversity was high (Ps?=?91%, APs?=?3.81, As?=?3.57 and Hes?=?0.352) as was mean population genetic diversity (Pp?=?81%, APp?=?2.98, Ap?=?2.59 and Hep?=?0.320) which ranks it among the highest 10% of plant species surveyed. Partitioning of genetic variation (Gst?=?0....

Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.

Pit lakes (abandoned flooded mine pits) represent a potential liability or valuable water resource to mining companies, the environment, and regional communities. However, water quality in the pit lakes can often restrict end uses for the water, particularly if affected by acid mine drainage (AMD). Nevertheless, various and diverse treatment strategies now exist for remediating the water quality of these significant post-mining landscape features. Backfilling of the pit may prevent the formation of a pit lake, or may be important in determining the final pit lake shape and bathymetry. Fast filling or contrived lake stratification may also reduce the extent of pyrite oxidation and hence acidity production. Some "active" remediation technologies such as direct liming of pit water are well-pr...

Mining activities create wastelands that require reclamation. The relief of abandoned opencast oil shale mining area is rugged, and the mining spoil is extremely stony and alkaline (pH 8), with low N and organic content. Planting of fast-growing deciduous tree species such as silver birch (Betula pendula) on post-mining area is the best means to accelerate the development of a new forest ecosystem in such harsh conditions. A chronosequence of silver birch stands (1, 2, 3, 5, 29, 40 years old) was investigated to reveal changes in bulk soil (S) and rhizosphere properties, in rhizosphere effect on bacterial activity and diversity, and in fine-root morphological adaptations in relation to stand development. The rhizosphere effect on bacterial activity was measured as a rhizosphere/soil (R/S) ...

The continuous improvement of crop plants is essential for agriculture in the coming decades and relies on the use of genetic variability through breeding. However, domestication and modern breeding have reduced diversity in the crop germplasm. Global gene banks conserve diversity, but these resourc...

Banana (Musa acuminata Colla. [AA, AAA]; Musa x paradisiaca Colla. [ABB, AAAB, AABB]), are large monocotyledonous plants in the Musaceae and is one of the world’s most important food crops. High genetic diversity can be found in centers of origin, but the lack of diversity in commercial production ...

The aim was to establish the genetic diversity and population structure of three guinea pig lines, from seven production zones located in Nariño, southwest Colombia. A total of 384 individuals were genotyped with six microsatellite markers. The measurement of intrapopulation diversity revealed allel...

Xanthomonas campestris pv. campestris infects a large number of cruciferous plants, including weeds. California has one of the largest and most diverse populations of wild cruciferous plants in the world. Although considerable information is available on the genetic diversity of X. campestris pv. ca...

Improving our knowledge of the links between ecology and evolution is especially critical in the actual context of global rapid environmental changes. A critical step in that direction is to quantify how variation in ecological factors linked to habitat modifications might shape observed levels of genetic variability in wild populations. Still, little is known on the factors affecting levels and distribution of genetic diversity at the individual level, despite its vital underlying role in evolutionary processes. In this study, we assessed the effects of habitat quality on population structure and individual genetic diversity of tree swallows (Tachycineta bicolor) breeding along a gradient of agricultural intensification in southern Québec, Canada. Using a landscape genetics approach, we found that individual genetic diversity was greater in poorer quality habitats. This counter-intuitive result was partly explained by the settlement patterns of tree swallows across the landscape. Individuals of higher genetic diversity arrived earlier on their breeding grounds and settled in the first available habitats, which correspond to intensive cultures. Our results highlight the importance of investigating the effects of environmental variability on individual genetic diversity, and of integrating information on landscape structure when conducting such studies. PMID:19414469

Hydrologic conditions near surface coal mines in southeastern Montana are being monitored because the coal beds are the most accessible and widely used aquifers of the region. Mining has thus far affected water levels in alluvium only locally, if at all. Water levels in coal-bed aquifers are being lowered within about 2 miles of active mines near Colstrip. As mine pits are backfilled with spoil, hydrostatic pressures in both the spoil and adjacent aquifers are recovering toward pre-mining levels. At Decker, a potentiometric depression has formed over an area more than 5 miles wide and 15 miles long, caused by converging of drawdowns created by 3 mines. At all mines, water-level declines clearly illustrate the influences of directional permeabilities and hydrologic boundaries. As pits are being backfilled, spoils are rapidly becoming resaturated by inflow from undisturbed aquifers, laterally at all mines, and vertically where conditions are appropriate. It is hypothesized that pre-mining non-plugged drill holes allow vertical flow. In the resaturation process, strongly increased concentrations of dissolved solids (primarily calcium, magnesium, sodium, and sulfate) are evolving. The initial chemical quality of spoils water is highly diverse because of the variable distribution of soluble salts in the spoils. As groundwater flow in the spoils continues, trends are becoming apparent. Some sites are currently showing increasing concentrations where surface recharge introduces dissolved solids faster than they are flushed from the system. Other sites show decreasing trends where new salts are not introduced by recharge. In these cases, chemical quality of spoils water may approach pre-mining quality within the predictable future.

Bacterial transformation is a programmed process resulting in genetic transfer and diversity. It relies on the development of competence via regulatory circuits which are diverse and tailored to the particular lifestyle of each species. Despite this diversity, some species have been reported to trigger competence in response to antibiotics. Here, we review these recent findings, which reinforce the view that competence is a stress response and can substitute for SOS in bacteria lacking it.

It has been well documented that baculovirus populations exhibit high levels of genetic variation. Due to the lack of sensitivity of the techniques currently used to study baculovirus genetic variation, relatively little is known about baculovirus genetic diversity at the individual insect level. Since denaturing gradient gel electrophoresis (DGGE) has key advantages over other methods used to study genetic variation in baculoviruses, DGGE assays were used to obtain a better understanding of the genetic variation within baculovirus populations in individual host insects. Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model baculovirus system, and neonate H. armigera larvae were infected with one of two geographically distinct HearNPV isolates. DGGE assays for two lepidopteran-specific baculovirus genes, me53 and dbp1, detected many HearNPV genetic variants within individual host larvae, with up to 20 genetic variants detected in a 434-bp fragment of the dbp1 gene in a single neonate larva. High levels of HearNPV genetic diversity were detected in individual host larvae irrespective of the HearNPV isolate used to infect the larvae. This study sets a benchmark for HearNPV genetic variation in individual H. armigera larvae. The levels of HearNPV genetic diversity detected are higher than reported previously for a baculovirus population at the individual insect level. PMID:22878553

Red clover (Trifolium pratense L.) is one of the most important forage species. The amount of genetic variation within species and populations and the distribution of genetic diversity (GD) among populations is important to breeders and biologists. The objective of this study was to assess GD in 15 ...

The architecture of natural variation present in a contemporary population is a result of multiple population genetic forces, including population bottleneck and expansion, selection, drift, and admixture. We seek to untangle the contribution of admixture to genetic diversity on the Micronesian isla...

The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P < 0.001) was found between agro-morphological and RAPD markers in estimating the genetic distance between populations. Both methods suggested the existence of a substantial amount of genetic diversity both in the Vietnamese and Cambodian populations. Although both agro-morphological and RAPD markers were found to be useful in genetic diversity analysis in sesame, their combined use would give superior results. PMID:21410468

Genetic and epigenetic variation is a key determinant of human diversity and has an impact on disease predisposition. Single nucleotide polymorphisms (SNPs) and copy number polymorphisms (CNPs) are the main forms of genetic variation. The challenge is to distinguish normal variations from disease...

The jungle habitat of the Temuan aborigines harbors a variety of infectious diseases, the most notable being malaria. Our study of 15 genetic systems in the Temuan revealed substantial polymorphism and within-population genetic diversity. The polymorphisms for Hb beta, G6PD, and El are of interest i...

The major histocompatibility system provides a unique genetic locus in vertebrates to assess genetic diversity and to look for the effects of selecti.on on the immune system. Fish population studies using MHC are fairly new, and thus far they have focused on endangered population...

This guide describes the development of genetic engineering and the work and achievements of genetic surgeons in which we place our hopes while fearing and dreading the outcome at the same time. Diverse arguments are compiled to help the reader form his own opinion. (orig./EF)

Peanut (Arachis hypogaea L.) is an important crop for oil production. In the recent years, molecular marker technologies have been widely applied to genetic diversity analysis, genetic mapping, molecular marker-assisted breeding, gene tagging and QTLs analysis. However, it is expensive, labor-intens...

Eighty-seven isolates of the sorghum ergot pathogen, C. africana, from diverse geographic locations were analyzed using four different AFLP primer combinations to determine genetic relationships among isolates. Most isolates showed unique AFLP types, indicating that much genetic variation is present...

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs. This study employed amplified fragment length polymorphism (AFLP) to investigate the genetic variation in local banana cultivars from the south...

Many works demonstrate the benefits of using highly polymorphic markers such as microsatellites in order to measure the genetic diversity between closely related breeds. But it is sometimes difficult to decide which genetic distance should be used. In this paper we review the behaviour of the main d...

The purpose of the study was to evaluate the possible genetic effect on vegetative propagation of Coffea canephora. Diversity for somatic embryogenesis (SE) ability was observed not only among two groups of C. canephora Pierre (Congolese and Guinean), but also within these different genetic groups. ...

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands and USA in order to conserve as much genetic diversity as possible for this breed. Genetic variability of HF collections within and between countries was assessed and compared with active male HF populations in ...

Variation in soil properties may influence diversity of invertebrate communities, a crucial component of every ecosystem, and their impact should be considered also in restoration management. Although most spoil heaps have been reclaimed after brown coal mining, some post-mining sites are left to natural succession. Little is known, however, about the effects of these two fundamentally different approaches on diversity of invertebrates inhabiting these stands. While controlling for habitat characteristics, we analyzed the effects of soil properties on species richness of seven invertebrate groups representing various trophic levels and diverse spatial niches at afforested spoil heaps and adjacent pits managed under these two basic restoration approaches in the North Bohemia Brown Coal Basi...

The genetic diversity and population structure of 20 Tunisian Lavandula stoechas L. and Lavandula multifida L. populations, from different bioclimates, were analysed by starch gel electrophoresis using seven isozymes. The genetic diversity within populations varied according to species. Variation in L. multifida was higher than that observed for L. stoechas, and exclusive alleles were detected for taxa.A high differentiation among populations, for each species, estimated by Wright's F-statistics was revealed. The genetic structure of populations from the same bioclimate was substantial. Nei's, R. [1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590] genetic distance among pairs of populations was low. The UPGMA cluster an...

Asthma disproportionally affects different ethnic/racial groups, with Puerto Ricans and African Americans suffering the highest asthma prevalence and morbidity, Mexicans the lowest, and non-Hispanic whites in between. Genome-wide association studies of asthma have found both shared and race/ethnic-specific genetic risks factors for asthma. However, the majority of genetic asthma research is performed in populations of European descent, which limits the benefits of genetic research to European populations. It is important to biomedical and clinical research to include more diverse and underrepresented populations. The rich genetic diversity of all populations can be leveraged to scientific advantage. For example, admixture mapping provides a more powerful approach than traditional genome-wide allelic association studies in discovering genetic associations for complex diseases. By being more inclusive we can achieve a better understanding of the genetics of asthma, address health disparities, and ensure that scientific advances will benefit populations worldwide. PMID:22970422

We have investigated the local and regional scale genetic structure of Siberian primrose (Primula nutans) populations in Northern Europe. The genetic diversity and structure of fifteen populations sampled from the Bothnian Bay in Finland, the Barents Sea in Norway and the White Sea in Russia were assessed using eleven microsatellite markers. We investigated the distribution of genetic variation within and between populations, and studied the local genetic structure using spatial autocorrelation analysis. We found very low genetic and allelic diversity in the Bothnian Bay and Barents Sea populations, and only slightly higher in the White Sea population. The level of genetic differentiation between the regions was very high, whereas differentiation between the populations within the regions ...

Habitat fragmentation and the associated reduction in connectivity between habitat patches are commonly cited causes of genetic differentiation and reduced genetic variation in animal populations. We used eight microsatellite markers to investigate genetic structure and levels of genetic diversity in a relict population of wood frogs (Lithobates sylvatica) in Rocky Mountain National Park, Colorado, where recent disturbances have altered hydrologic processes and fragmented amphibian habitat. We also estimated migration rates among subpopulations, tested for a pattern of isolation-by-distance, and looked for evidence of a recent population bottleneck. The results from the clustering algorithm in Program STRUCTURE indicated the population is partitioned into two genetic clusters (subpopulatio...

Background and Aims Populations established by long-distance colonization are expected to show low levels of genetic variation per population, but strong genetic differentiation among populations. Whether isolated populations indeed show this genetic signature of isolation depends on the amount and diversity of diaspores arriving by long-distance dispersal, and time since colonization. For ferns, however, reliable estimates of long-distance dispersal rates remain largely unknown, and previous studies on fern population genetics often sampled older or non-isolated populations. Young populations in recent, disjunct habitats form a useful study system to improve our understanding of the genetic impact of long-distance dispersal. Methods Microsatellite markers were used to analyse the amount a...

Recently, high profile cases of financial statement fraud have been dominating the news. This paper uses data mining techniques such as Multilayer Feed Forward Neural Network (MLFF), Support Vector Machines (SVM), Genetic Programming (GP), Group Method of Data Handling (GMDH), Logistic Regression (L...

The bibliography contains citations concerning sources and potential genetic effects of arsenic. The citations discuss environmental sources, such as industrial waste and mining wastes, and examine how arsenic damages the chromosomes. The citations cite various outcomes as a result of such chromosome damage. (Contains 50-250 citations and includes a subject term index and title list.) (Copyright NERAC, Inc. 1995)

Papers are presented which reflect research in the following areas: development of the concept of technology assessment; institutionalization of technology assessment; the interface between law and technology assessment; and assessment case studies. Case studies include hazards of the medical use of X-rays, environmental noise effects in transportation planning, genetic technology, impact of underground coal mining, and aircraft/airport noise abatement.

ABSTRACT: BACKGROUND: Sesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC). RESULTS: Results from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven. CONCLUSIONS: This study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame. PMID:23153260

Abstract Homothallic Fusarium graminearum (teleomorph Gibberella zeae) and anamorphic F. culmorum are destructive pathogens causing Fusarium head blight (FHB) of small-grain cereals worldwide, while heterothallic F. pseudograminearum (G. coronicola) seems to be restricted to Australia as a FHB pathogen. In a comprehensive treatise of pathogen population genetics, this review summarizes global knowledge of genetic diversity among isolates sampled at various spatial and temporal scales, examines the mechanisms that generate this diversity and explores the implications of pathogen diversity and plasticity to resistance breeding. Despite their different modes of reproduction, there is large variation among isolates of all three species originating from different countries and continents. With ...

Abstract A large portion of the surface-ocean biomass is represented by microscopic unicellular plankton. These organisms are functionally and morphologically diverse, but it remains unclear how their diversity is generated. Species of marine microplankton are widely distributed because of passive transport and lack of barriers in the ocean. How does speciation occur in a system with a seemingly unlimited dispersal potential? Recent studies using planktonic foraminifera as a model showed that even among the cryptic genetic diversity within morphological species, many genetic types are cosmopolitan, lending limited support for speciation by geographical isolation. Here we show that the current two-dimensional view on the biogeography and potential speciation mechanisms in the microplankton ...

The continuum formed by Corsica and Sardinia is considered a biodiversity hotspot, and provides a model system to address the impact of long-term isolation on genetic diversity and gene flow. This study, based on two cpDNA noncoding sequences, investigated the evolution of Cistus creticus diversity on both islands. Populations of C. creticus separated into two distinct groups, and the ancestral origin group appeared to be located in central Corsica. The low gene flow and significant genetic diversity between these two groups was correlated with geological events that have characterized these two islands

Genetic diversity, population structure and genome-wide marker-trait association analysis was conducted for the USDA pea (Pisum sativum L.) core collection. The core collection contained 285 accessions with diverse phenotypes and geographic origins. The 137 DNA markers included 102 polymorphic fragments amplified by 15 microsatellite primer pairs, 36 RAPD loci and one SCAR (sequence characterized amplified region) marker. The 49 phenotypic traits fall into the categories of seed macro- and micro-nutrients, disease resistance, agronomic traits and seed characteristics. Genetic diversity, population structure and marker-trait association were analyzed with the software packages PowerMarker, STUCTURE and TASSEL, respectively. A great amount of variation was revealed by the DNA markers at the ...

Current patterns of genetic and morphological diversity are the product of historical climatic and geomorphological events, and of contemporary selection processes acting upon this diversity. Here we examine the phylogeographic and phenotypic patterns of diversity within Percichthys trucha, a widely distributed Patagonian fish species complex that inhabits Andean and steppe freshwater environments. Molecular analysis (mtDNA control region) of 21 populations distributed throughout its latitudinal range revealed little evidence of phylogeographic structure and no evidence of species-level genetic divergence east of the Andes. The complex, however, exhibits high levels of intra- and interpopulation phenotypic variation. Patterns of among-population divergence in morphology were most easily ex...

The influence of climate on biodiversity is an important ecological question. Various theories try to link climate change to allelic richness and therefore to predict the impact of global warming on genetic diversity. We model the relationship between genetic diversity in the European beech forests and curves of temperature and precipitation reconstructed from pollen databases. Our model links the genetic measure to the climate curves through a linear functional regression. The interaction in climate variables is assumed to be bilinear. Since the data are georeferenced, our methodology accounts for the spatial dependence among the observations. The practical issues of these extensions are discussed.

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Pleistocene for the Qinghai-Tibetan (Tibetan) plateau, a region where glaciation was not synchronous with the North Hemisphere ice sheet maxima, remains poorly understood. Here, we compared the phylogeographical patterns of five avian species on the Qinghai-Tibetan plateau by three mitochondrial DNA fragments: the Tibetan snow finch (Montifringilla adamsi), the Blanford's snow finch (Pyrgilauda blanfordi), the horned lark (Eremophila alpestris), the twite (Carduelis flavirostris) and the black redstart (Phoenicurus ochruros)...

PCR and sequencing artefacts can seriously bias population genetic analyses, particularly of populations with low genetic variation such as endangered vertebrate populations. Here, we estimate the error rates, discuss their population genetics implications, and propose a simple detection method that helps to reduce the risk of accepting such errors. We study the major histocompatibility complex (MHC) class IIB of guppies, Poecilia reticulata and find that PCR base misincorporations inflate the apparent sequence diversity. When analysing neutral genes, such bias can inflate estimates of effective population size. Previously suggested protocols for identifying genuine alleles are unlikely to exclude all sequencing errors, or they ignore genuine sequence diversity. We present a novel and stat...

Despite their ubiquity and importance to intertidal ecosystems, information is currently lacking regarding the genetic diversity of trematode parasites within coastal organisms and the distribution of their genetic variation among intertidal habitats. In this study, we quantified the clonal diversity of the coastal marine trematode Maritrema novaezealandensis within Zeacumantus subcarinatus snail hosts from three coastal bays in Otago Harbour, New Zealand, using five microsatellite loci to determine if differences exist in the frequency of occurrence of multi-clone infections. In addition, we examined gene flow among M. novaezealandensis collected from the three bays. The frequency of mixed-clone infections varied fourfold among bays and no genetic differentiation was detected among intert...

Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity. PMID:11162803

Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and d{sub N}/d{sub S} ratios (0.092) for interhost diversity were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks.

Abstract An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow sa...

In this study, the samples were collected from nine ETPs and soil contaminated with petroleum products. The genetic diversity of 30 Stenotrophomonas isolates was demonstrated by phylogenetic analysis of their 16S rRNA gene nucleotide sequences, and randomly amplified polymorphic DNA (RAPD) analysis supplemented with in silico signature and restriction enzyme (REs - AluI, BfaI, DpnII, HaeIII, RsaI and Tru9I) digestion analyses. Genetic diversity based on nucleotide sequence data revealed distinct clusters. Functional diversity was analysed on the basis of the abilities of these isolates to degrade phenol, p-cresol, catechol, 4-methylcatechol and hydroquinone. Based on the environmental, genetic and functional diversities, a consortium of mixed defined microbes has been proposed for bioremediation programs. PMID:20554196

Eucommia ulmoides, the only species of Eucommiaceae, has been used as Chinese medicinal plant for more than 2,000 years, and is endangered as a consequence of long-term overexploitation. In this study, genetic diversity within and among the semi-wild and cultivated populations of E. ulmoides collected from its main production area was investigated using two cpSSR and 227 AFLP loci. A moderate level of within-population diversity was observed (hS = 0.549 for cpSSR and H eB = 0.183 for AFLPs), which could be explained by the dioecious breeding system, longevity, and human mediated seed exchange. Compared to the semi-wild population, the cultivated population possessed relatively low genetic diversity, which suggests cultivation practice may have reduced the genetic diversity of E. ulmoides. ...

By using denaturing gradient gel electrophoresis (DGGE) and Biolog_Eco micro-plate technique, this paper studied the soil microbial genetic taxonomic and bacterial metabolic functional diversities under four de-farming patterns, i. e., natural restoration (NT, dominant plant species Neyraudia reynaudiana and Miscanthus floridulus), economic plantation (CM, Cajanus cajan and Castanea mollissima), zero-tillage (PI, Pennisetum purpureum and Zenia insign), and conventional tillage (MB, maize-soybean intercropping), in a typical Karst peak-cluster depression. All test de-farming patterns had significant effects on the soil microbial community structure and bacterial metabolic pattern. The community structure of soil fungi was more affected by the de-farming patterns than that of soil bacteria, while the later was more affected by seasonal variation. After 6-7 years of de-farming, soil bacterial taxonomic Shannon diversity indices had no significant differences under the four de-farming patterns, while soil fungal taxonomic Shannon diversity indices were significantly higher under CM and PI than under NT and MB. The soil bacterial metabolic functional diversity under PI was obviously lower than those under other de-farming patterns. Therefore, soil fungal genetic and bacterial metabolic diversities were more sensitive to de-farming patterns than soil bacterial genetic diversity did. Among the four de-farming patterns, economic plantation had the superiority in maintaining soil microbial genetic and bacterial metabolic functional diversities, being a better de-farming pattern. PMID:20462000

In the present study, we analyze the genetic structure and diversity among accessions of popcorn obtained from the CIMMYT International Maize and Wheat Improvement Center that represent the diversity available for current use by breeding programs. The main objectives were to identify SSR loci that were the best indicators of genetic diversity, to measure the genetic diversity within popcorn genotypes, and to analyze the genetic structure of the promising populations destined for use in breeding programs. The mean gene diversity of all SSR loci was 0.6352. An extremely high population differentiation level was detected (F ( st ) = 0.3152) with F ( st ) for each locus ranging from 0.1125 (Umc1229) to 0.4870 (Umc1755). Analyzing the genetic structure of eight popcorn accessions was especially important for identifying both SSR loci with high levels of heterozygosity and genotypes showing high heterozygosity (BOYA: 462 and ARZM: 13 050). This analysis should be the medium and long-term selection goal for the generation of inbred lines and the future production of new cultivars. Plant accessions ARZM: 05 083, ARZM: 13 050, and URUG: 298 may also be useful varieties that exhibit important agronomic characteristics that can be used through crosses to broaden the genetic basis of popcorn. PMID:22467122

The Surface Mining Control and Reclamation Act of 1977 requires that coal mine sites in the United States be reclaimed to establish vegetative cover that is diverse, native, and capable of plant succession. However, there is a question as to whether vegetation established on coal mine sites reclaimed with biosolids is diverse and capable of plant succession. The influx of nutrients with the addition of biosolids leads to long-term dominance by early-successional species, most notably grasses, and consequently, a low establishment of woody and volunteer species. Additionally, many grass species commonly planted in reclamation have aggressive growth habits that lead to their dominance in coal mine plant communities. The establishment and growth of selected grass mixes was evaluated to determine whether alternative grass mixes would be less competitive with woody and volunteer species as compared to commonly used grass mixes. Percent vegetative cover, species richness, and the survival of direct-seeded woody species were assessed for each treatment grass mixture. It was found that Poa compress and a mixture of P. compress, Panicum virgatum, and Trifolium repens provided adequate coverage while still allowing the highest species richness and survival of woody species. Use of these species mixtures in coal mine reclamation with biosolids in the eastern United States would likely lead to establishment of a more species-rich plant community with a greater woody species component while still providing erosion control and site protection.

It is not known if current chemical and biological monitoring methods are appropriate for assessing the impacts of growing industrial development on ecologically sensitive northern waters. We used a multitrophic level approach to evaluate current monitoring methods and to determine whether metal-mining activities had affected 2 otherwise pristine rivers that flow into the South Nahanni River, Northwest Territories, a World Heritage Site. We compared upstream reference conditions in the rivers to sites downstream and further downstream of mines. The endpoints we evaluated included concentrations of metals in river water, sediments, and liver and flesh of slimy sculpin (Cottus cognatus); benthic algal and macroinvertebrate abundance, richness, diversity, and community composition; and various slimy sculpin measures, our sentinel forage fish species. Elevated concentrations of copper and iron in liver tissue of sculpin from the Flat River were associated with high concentrations of mine-derived iron in river water and copper in sediments that were above national guidelines. In addition, sites downstream of the mine on the Flat River had increased algal abundances and altered benthic macroinvertebrate communities, whereas the sites downstream of the mine on Prairie Creek had increased benthic macroinvertebrate taxa richness and improved sculpin condition. Biological differences in both rivers were consistent with mild enrichment of the rivers downstream of current and historical mining activity. We recommend that monitoring in these northern rivers focus on indicators in epilithon and benthic macroinvertebrate communities due to their responsiveness and as alternatives to lethal fish sampling in habitats with low fish abundance. We also recommend monitoring of metal burdens in periphyton and benthic invertebrates for assessment of exposure to mine effluent and causal association. Although the effects of mining activities on riverine biota currently are limited, our results show that there is potential for effects to occur with proposed growth in mining activities. PMID:18597569

American ginseng (Panax quinquefolius) is a native North American medicinal plant that is becoming increasingly vulnerable despite government harvest restrictions. To better understand the genetic diversity and gene flow of American ginseng, we studied RAPD variation in cultivated and wild populations. Classical and Bayesian analogues of genetic diversity statistics were estimated in seven wild and two cultivated populations. The wild populations were more highly structured (G st?  = 0.41) than the cultivated populations (G st?  = 0.24). The genetic diversity within populations ranged from H e?  = 0.05 to 0.38. Based on genetic pairwise distances, six of the wild populations clustered with the locally-derived cultivated population, while one wild population was more similar to the non-loca...

Summary The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average FST of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Ha...

Amplified fragment length polymorphism markers were evaluated to determine the genetic diversity and relationships among cultivated and weedy ryes (Secale cereale L.) using a large global set of accessions. On the basis of 395 polymorphic bands resulted from nine PstI-MseI primer combinations, cultivated rye exhibited higher average genetic diversity (Ht = 0.34) than that of the weedy rye (Ht = 0.27), however, it had lower genetic differentiation (Fst = 0.16). The average genetic diversity of cultivated rye varied from region to region ranging from 0.21 to 0.31. As expected, all cultivated accessions clustered together both in dendrogram and principal coordinate diagram indicating common breeding program selection criteria based on similar value-added agronomic characteristics. A clu...

Abstract in english Habitat fragmentation may cause population subdivision, affecting genetic variation, leading to heterozygosity loss and increased inbreeding, and contributing to population extinction. However, some genetic models have shown that under some conditions, population subdivision can favor heterozygosity and allelic diversity, and small populations may adapt to inbreeding. Here I investigate the relationship between population subdivision and genetic diversity for the marsupia (more) l Micoureus paraguayanus (Tate, 1931) using the program Vortex. Hypothetical populations of 100 and 2000 individuals were partitioned into 1, 2, 5 or 10 populations that were linked by varying rates of dispersal and also by sex-biased dispersal. Results suggested that heterozygosity and allelic diversity declined rapidly when a population was subdivided. Genetic and demographic stochasticity diminished the effectiveness of selection against recessive lethal alleles. Dispersal partly reversed the impacts of population subdivision. However, even high rates of dispersal did not eliminate demographic fluctuations or prevent extinction. Although gene flow largely prevented genetic divergence between populations, dispersal did not prevent heterozygosity from being lost more rapidly in subdivided populations than in single populations of equivalent total size. The dynamics of small, fragmented populations were critically dependent on interactions between demographic and genetic processes. Populations of M. paraguayanus may have to be relatively large and continuous to avoid significant losses of genetic diversity.

Levoglucosan (LG) is emitted into the environment only during the combustion of wood and cigarettes. As such, it is a useful tracer for wood smoke in the atmosphere. It also has potential use as a fermentative carbon and energy resource in the fermentation industry. Depending on the initial cellulose content of woody feedstocks, the yield of LG may range from 38 to 58 per cent. This study examined whether the LG-assimilating bacterium could be isolated or not under LG treatment. The study also addressed the impact of the LG on the genetic diversity and the diversity of the cultivable fraction of the bacterial community in soil suspension. Genetic diversity was analyzed by Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting. The changes in diversity were monitored by two different methods following a 90 day incubation period for 20 mg of LG per mL of soil suspension. The cultivable heterotrophic diversity was investigated by colony morphology on solid 1/5 lactobacillus medium. The results of the cultivable heterotrophic diversity and genetic diversity showed that there was an obvious decrease in diversity, and the amount of levoglucosan-assimilating bacteria also decreased. The application of LG had an obvious impact on Bacillus spp and Marinibacillus spp. Through cultivable analysis, five levoglucosan-assimilating bacteria were isolated from an LG treated soil suspension. Phylogenetic analysis of 16S rRNA gene sequences revealed that levoglucosan-assimilating bacteria belong to Bacillus and Marinibacillus. 2 refs., 2 tabs., 3 figs.

ABSTRACT: BACKGROUND: Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. RESULTS: According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. CONCLUSIONS: A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits. PMID:22510209

The diversity of planktonic microorganisms in fluids from a group of flowing subterranean boreholes was monitored from the day they were drilled to as long as three and a half months after drilling as they drained into Evander Au mine. Geochemical analyses of the water, characterization of microbial communities by phospholipids fatty acid (PLFA) and DNA sequence analyses, and calculations of free energy flux indicated that mine-introduced microbial contaminants, dominated by ? and ? Proteobacteria, Cenarchaeaceae and Candidatus Nitrososphaera, were flushed from the boreholes and replaced by fracture water derived microbial communities dominated by Firmicutes, Methanosarcinalesand Thermoproteaceaea. The fracture water was a mixture of paleometeoric water and 2.0 Ga old, diagenet...

Questions of control of banks are examined on the basis of geomechanical validation of optimum parameters of tailing slopes. Principles of control of banks are formulated, composition and structure of bank facilities are examined, creep deformations of banks under diverse mining and geologic conditions are analyzed, and factors which determine stability of the banks and hydraulic banks are established. Simple, reliable, rather accurate methods of computation of stability of tailing slopes most useful in mining practice are described. Two groups of methods of control of slopes are presented and conditions of use of each of the methods are determined.

By adopting antimicrobial spectrum test, BOXAIR-PCR, physiological and biochemical, and 16S rDNA sequencing analysis, this paper analyzed the diversity of 55 antagonistic bacterial strains isolated from the rhizosphere of 10 cash crops. There was a high diversity of the antagonism of the strains. Based on BOXAIR-PCR, all the strains were clustered into 7 groups at the similarity level of 72.1%, and divided into 25 groups at the similarity level of 85.0%. All the strains belonged to Bacillus, Paenibacillus, Brevibacillus, Pseudomonas and Alcaligenes, respectively. The antagonistic bacteria isolated from the rhizosphere had high genetic diversity and high diversity in antagonistic activity. PMID:22586980

A method to quantify the contribution of subpopulations to genetic diversity in the whole population was assessed using pedigree information. The standardization of between- and within-subpopulation mean coancestries was developed to account for the different coat colour subpopulation sizes in the Spanish Purebred (SPB) horse population. The data included 166264 horses registered in the SPB Studbook. Animals born in the past 11 years (1996 to 2006) were selected as the 'reference population' and were grouped according to coat colour into eight subpopulations: grey (64 836 animals), bay (33 633), black (9414), chestnut (1243), buckskin (433), roan (107), isabella (57) and white (37). Contributions to the total genetic diversity were first assessed in the existing subpopulations and later compared with two scenarios with equal subpopulation size, one with the mean population size (13 710) and another with a low population size (100). Ancestor analysis revealed a very similar origin for the different groups, except for six ancestors that were only present in one of the groups likely to be responsible for the corresponding colour. The coancestry matrix showed a close genetic relationship between the bay and chestnut subpopulations. Before adjustment, Nei's minimum distance showed a lack of differentiation among subpopulations (particularly among the black, chestnut and bay subpopulations) except for isabella and white individuals, whereas after adjustment, white, roan and grey individuals appeared less differentiated. Standardization showed that balancing coat colours would contribute preserving the genetic diversity of the breed. The global genetic diversity increased by 12.5% when the subpopulations were size standardized, showing that a progressive increase in minority coats would be profitable for the genetic diversity of this breed. The methodology developed could be useful for the study of the genetic structure of subpopulations with unbalanced sizes and to predict their genetic importance in terms of their contribution to genetic variability. PMID:22444259

Weedy rice has been becoming a notorious weed in the paddy field of China in recent decades due to its increasing damage to rice yield and rice quality. In this study, a microsatellite technique with 21 pairs of SSR markers was utilized to estimate the genetic structure of two biotypes of weedy rice with Japonica and Indica rice characteristics, collected from Liaoning and Guangdong provinces, respectively. The genetic diversity of the weedy rice in the two provinces was relatively low (Liaoning h?=?0.086; Guangdong h?=?0.160), and distinctly large genetic differences existed between these two provinces (Gcs?=?0.623). The genetic diversity was found primarily within populations, and genetic differentiation was relatively low within the same province. Both cluster analysis (UPGMA) and princ...

Genetic diversity is essential to crop improvement. However, lack of molecular markers prevents the understanding of genetic diversity in celery and related species. In this study, SRAP and SSR markers was firstly used to evaluate genetic variation in 68 accessions of Apium graveolens and related species. A total of 888 bands were generated by 40 primer combinations of SRAP and 32 bands were produced by eight SSR markers. Of the 920 bands, 95.1% were polymorphic between A. graveolens and related species, and 49.2% were polymorphic within A. graveolens. Cluster and structure analysis could distinguish local celery, celery, and related species. These results suggested that both SRAP and SSR technologies can be efficiently used to characterize genetic variation and analyze genetic relationshi...

Extremely large accumulation of green algae Enteromorpha prolifera floated along China' coastal region of the Yellow Sea ever since the summer of 2008. Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea. Two hundred reproducible fragments were generated with 8 AFLP primer combinations, of which 194 (97%) were polymorphic. The average Nei's genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations. The E. prolifera originated from different areas and were undergoing a course of mixing.

To assess the genetic diversity and genetic structure of East Asian wild radish (Raphanus sativus var. hortensis f. raphanistroides), 13 natural populations from Japan and Korea were analyzed for amplified fragment length polymorphism (AFLP). On the average, 77.4% of the AFLP markers generated by eight primer pairs were polymorphic. Both Japanese and Korean populations of wild radish showed a high within population variation (66.3% polymorphic markers, Shannon’s information index HO = 3.486, and genetic diversity HEP = 0.128). The majority of the genetic variation of wild radish (96.7%) was observed within populations. Although no appreciable local differentiation of AFLP markers was detected, AFLP markers were more effective than allozymes in classifying natural populations of East Asian wild radish. AFLP variation showed a very close genetic relationship between R. raphanistrum and R. sativus, particularly Kazakhstan R. sativus, confirming the assumption that R. raphanistrum might be involved in the origin of R. sativus.   

To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms. From the metagenome sequences of an anaerobic microbial community actively decaying poplar biomass, we identified approximately 4,000 GHase homologs. Based on homology to GHase families/activities of interest and the quality of the sequences, candidates were selected for full-length cloning and subsequent expression. As an alternative strategy, a metagenome expression library was constructed and screened for GHase activities. These combined efforts resulted in the cloning of four novel GHases that could be successfully expressed in Escherichia coli. Further characterization showed that two enzymes showed significant activity on p-nitrophenyl-{alpha}-L-arabinofuranoside, one enzyme had significant activity against p-nitrophenyl-{beta}-D-glucopyranoside, and one enzyme showed significant activity against p-nitrophenyl-{beta}-D-xylopyranoside. Enzymes were also tested in the presence of ionic liquids. Metagenomics provides a good resource for mining novel biomass degrading enzymes and for screening of cellulolytic enzyme activities. The four GHases that were cloned may have potential application for deconstruction of biomass pretreated with ionic liquids, as they remain active in the presence of up to 20% ionic liquid (except for 1-ethyl-3-methylimidazolium diethyl phosphate). Alternatively, ionic liquids might be used to immobilize or stabilize these enzymes for minimal solvent processing of biomass.

Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and HE were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term Ne varied from 92.4 individuals under the linkage disequilibrium model to under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.

Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST-SSRs) with a motif length of 1-6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST-SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST-SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies. PMID:16924545

Castor and Jatropha belong to the Euphorbiaceae family. This review highlights the role of biotechnological tools in the genetic improvement of castor and jatropha. Castor is monotypic and breeding programmes have mostly relied on the variability available in the primary gene pool. The major constraints limiting profitable cultivation are: vulnerability to insect pests and diseases, and the press cake is toxic which restrict its use as cattle feed. Conventional breeding techniques have limited scope in improvement of resistance to biotic stresses and in quality improvement owing to low genetic variability for these traits. Genetic diversity was assessed using protein based markers while use of molecular markers is at infancy. In vitro studies in castor have been successful in shoot proliferation from meristematic explants, but not callus-mediated regeneration. Genetic transformation experiments have been initiated for development of insect resistant and ricin-free transgenics with very low transformation frequency. In tropical and subtropical countries jatropha is viewed as a potential biofuel crop. The limitations in available germplasm include; lack of knowledge of the genetic base, poor yields, low genetic diversity and vulnerability to a wide array of insects and diseases. Great scope exists for genetic improvement through conventional methods, induced mutations, interspecific hybridization and genetic transformation. Reliable and highly efficient tissue culture protocols for direct and callus-mediated shoot regeneration and somatic embryogenesis are established for jatropha which indicates potential for widening the genetic base through biotechnological tools. Assessment of genetic diversity using molecular markers disclosed low interaccessional variability in local Jatropha curcas germplasm. The current status and future prospects of in vitro regeneration, genetic transformation and the role of molecular tools in the genetic enhancement of the two-oilseed crops are discussed. PMID:18579331

Coffea canephora Pierre ex Frohener is a perennial plant originated from Africa. Two main groups, Guinean and Congolese, have already been identified within this species. They correspond to main refugia in western and central Africa. In this paper we present the analysis of a region that has not yet been studied, Uganda. Two wild, one feral (once cultivated but abandoned for many years), and two cultivated populations of C. canephora from Uganda were evaluated using 24 microsatellite markers. Basic diversity, dissimilarity and genetic distances between individuals, genetic differentiation between populations, and structure within populations were analysed. Expected heterozygosity was high for wild compartments (0.48 to 0.54) and for cultivated and feral ones (0.57 to 0.59), with the number of private alleles ranging from 12 for cultivated genotypes to 37 for a wild compartment. The Ugandan samples show significant population structuring. We compared the Ugandan populations with a representative sample of known genetic diversity groups within the species using 18 markers. Coffea canephora of Ugandan origin was found to be genetically different from previously identified diversity groups, implying that it forms another diversity group within the species. Given its large distribution and extremely recent domestication, C. canephora can be used to understand the effect of refugia colonization on genetic diversity. PMID:19767894