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Sample records for affect genetic diversity

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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) of this population of honey bee queens to be 13.6 ± 6.76, which was not significantly different between colonies that superseded their queen and those that did not.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

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

    PubMed

    Tarpy, David R; Vanengelsdorp, Dennis; Pettis, Jeffrey S

    2013-08-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Honey bee (Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirica...

  4. Factors affecting levels of genetic diversity in natural populations.

    PubMed Central

    Amos, W; Harwood, J

    1998-01-01

    Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered 'normal', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be

  5. Ex situ cultivation affects genetic structure and diversity in arable plants.

    PubMed

    Brütting, C; Hensen, I; Wesche, K

    2013-05-01

    Worldwide, botanical gardens cultivate around 80,000 taxa, corresponding to approximately one-quarter of all vascular plants. Most cultivated taxa are, however, held in a small number of collections, and mostly only in small populations. Lack of genetic exchange and stochastic processes in small populations make them susceptible to detrimental genetic effects, which should be most severe in annual species, as sowing cycles are often short. In order to assess whether ex situ cultivation affects genetic diversity of annuals, five annual arable species with similar breeding systems were assessed with 42 in situ populations being compared to 20 ex situ populations using a random amplified polymorphic DNA (RAPD) analysis approach. Population sizes tended to be lower under ex situ cultivation and levels of genetic diversity also tended to be lower in four of the five species, with differences being significant in only two. Ex situ populations showed incomplete representation of alleles found in the wild. The duration of cultivation did not indicate any effect on genetic diversity. This implies that cultivation strategies resulted in different genetic structures in the garden populations. Although not unequivocally pronounced, differences nonetheless imply that conservation strategies in the involved gardens may need improvement. One option is cold storage of seeds, a practice that is not currently followed in the studied ex situ collections. This may reflect that the respective gardens focus on displaying living plant populations.

  6. Landscape context affects genetic diversity at a much larger spatial extent than population abundance.

    PubMed

    Jackson, Nathan D; Fahrig, Lenore

    2014-04-01

    Regional landscape context influences the fate of local populations, yet the spatial extent of this influence (called the "scale of effect") is difficult to predict. Thus, a major problem for conservation management is to understand the factors governing the scale of effect such that landscape structure surrounding a focal area is measured and managed at the biologically relevant spatial scale. One unresolved question is whether and how scale of effect may depend on the population response measured (e.g., abundance vs. presence/absence). If scales of effect differ across population outcomes of a given species, management based on one outcome may compromise another, further complicating conservation decision making. Here we used an individual-based simulation model to investigate how scales of effect of landscapes that vary in the amount and fragmentation of habitat differ among three population responses (local abundance, presence/absence, and genetic diversity). We also explored how the population response measured affects the relative importance of habitat amount and fragmentation in shaping local populations, and how dispersal distance mediates the magnitude and spatial scale of these effects. We found that the spatial scale most strongly influencing local populations depended on the outcome measured and was predicted to be small for abundance, medium-sized for presence/absence, and large for genetic diversity. Increasing spatial scales likely resulted from increasing temporal scales over which outcomes were regulated (with local genetic diversity being regulated over the largest number of generations). Thus, multiple generations of dispersal and gene flow linked local population patterns to regional population size. The effects of habitat amount dominated the effects of fragmentation for all three outcomes. Increased dispersal distance strongly reduced abundance, but not presence/absence or genetic diversity. Our results suggest that managing protected species

  7. Genetic diversity affects the strength of population regulation in a marine fish.

    PubMed

    Johnson, D W; Freiwald, J; Bernardi, G

    2016-03-01

    Variation is an essential feature of biological populations, yet much of ecological theory treats individuals as though they are identical. This simplifying assumption is often justified by the perception that variation among individuals does not have significant effects on the dynamics of whole populations. However, this perception may be skewed by a historic focus on studying single populations. A true evaluation of the extent to which among-individual variation affects the dynamics of populations requires the study of multiple populations. In this study, we examined variation in the dynamics of populations of a live-bearing, marine fish (black surfperch; Embiotoca jacksoni). In collaboration with an organization of citizen scientists (Reef Check California), we were able to examine the dynamics of eight populations that were distributed throughout approximately 700 km of coastline, a distance that encompasses much of this species' range. We hypothesized that genetic variation within a local population would be related to the intensity of competition and to the strength of population regulation. To test this hypothesis, we examined whether genetic diversity (measured by the diversity of mitochondrial DNA haplotypes) was related to the strength of population regulation. Low-diversity populations experienced strong density dependence in population growth rates and population sizes were regulated much more tightly than they were in high-diversity populations. Mechanisms that contributed to this pattern include links between genetic diversity, habitat use, and spatial crowding. On average, low-diversity populations used less of the available habitat and exhibited greater spatial clustering (and more intense competition) for a given level of density (measured at the scale of the reef). Although the populations we studied also varied with respect to exogenous characteristics (habitat complexity, densities of predators, and interspecific competitors), none of these

  8. Does population size affect genetic diversity? A test with sympatric lizard species

    PubMed Central

    Hague, M T J; Routman, E J

    2016-01-01

    Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations. PMID:26306730

  9. Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

    PubMed Central

    Dias, Armando Cavalcante Franco; Pereira e Silva, Michele de Cassia; Cotta, Simone Raposo; Dini-Andreote, Francisco; Soares, Fábio Lino; Salles, Joana Falcão; Azevedo, João Lúcio; van Elsas, Jan Dirk

    2012-01-01

    Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies. PMID:22941088

  10. Host and vector movement affects genetic diversity and spatial structure of Buggy Creek virus (Togaviridae).

    PubMed

    Brown, Charles R; Bomberger Brown, Mary; Padhi, Abinash; Foster, Jerome E; Moore, Amy T; Pfeffer, Martin; Komar, Nicholas

    2008-05-01

    Determining the degree of genetic variability and spatial structure of arthropod-borne viruses (arboviruses) may help in identifying where strains that potentially cause epidemics or epizootics occur. Genetic diversity in arboviruses is assumed to reflect relative mobility of their vertebrate hosts (and invertebrate vectors), with highly mobile hosts such as birds leading to genetic similarity of viruses over large areas. There are no empirical studies that have directly related host or vector movement to virus genetic diversity and spatial structure. Using the entire E2 glycoprotein-coding region of 377 Buggy Creek virus isolates taken from cimicid swallow bugs (Oeciacus vicarius), the principal invertebrate vector for this virus, we show that genetic diversity between sampling sites could be predicted by the extent of movement by transient cliff swallows (Petrochelidon pyrrhonota) between nesting colonies where the virus and vectors occur. Pairwise F(ST) values between colony sites declined significantly with increasing likelihood of a swallow moving between those sites per 2-day interval during the summer nesting season. Sites with more bird movement between them had virus more similar genetically than did pairs of sites with limited or no bird movement. For one virus lineage, Buggy Creek virus showed greater haplotype and nucleotide diversity at sites that had high probabilities of birds moving into or through them during the summer; these sites likely accumulated haplotypes by virtue of frequent virus introductions by birds. Cliff swallows probably move Buggy Creek virus by transporting infected bugs on their feet. The results provide the first empirical demonstration that genetic structure of an arbovirus is strongly associated with host/vector movement, and suggest caution in assuming that bird-dispersed arboviruses always have low genetic differentiation across different sites.

  11. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations

    PubMed Central

    Shilova, Irina N.; Robidart, Julie C.; DeLong, Edward F.; Zehr, Jonathan P.

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics. PMID:26751368

  12. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations.

    PubMed

    Shilova, Irina N; Robidart, Julie C; DeLong, Edward F; Zehr, Jonathan P

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.

  13. Genetic diversity in Gossypium genus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The overall objectives of this paper are to report on cotton germplasm resources, morphobiological and agronomic diversity of Gossypium genus and review efforts on molecular genetic diversity of cotton gene pools as well as on the challenges and perspectives of exploiting genetic diversity in cotton...

  14. An Anthropocene map of genetic diversity.

    PubMed

    Miraldo, Andreia; Li, Sen; Borregaard, Michael K; Flórez-Rodríguez, Alexander; Gopalakrishnan, Shyam; Rizvanovic, Mirnesa; Wang, Zhiheng; Rahbek, Carsten; Marske, Katharine A; Nogués-Bravo, David

    2016-09-30

    The Anthropocene is witnessing a loss of biodiversity, with well-documented declines in the diversity of ecosystems and species. For intraspecific genetic diversity, however, we lack even basic knowledge on its global distribution. We georeferenced 92,801 mitochondrial sequences for >4500 species of terrestrial mammals and amphibians, and found that genetic diversity is 27% higher in the tropics than in nontropical regions. Overall, habitats that are more affected by humans hold less genetic diversity than wilder regions, although results for mammals are sensitive to choice of genetic locus. Our study associates geographic coordinates with publicly available genetic sequences at a massive scale, yielding an opportunity to investigate both the drivers of this component of biodiversity and the genetic consequences of the anthropogenic modification of nature.

  15. EPA'S GENETIC DIVERSITY RESEARCH PROGRAM: ECOLOGICAL INDICATOR DEVELOPMENT

    EPA Science Inventory

    Genetic diversity is a fundamental component of biodiversity that is affected by environmental stressors in predictable ways and limits potential responses of a population to future stressors. Understanding patterns of genetic diversity enhances the value and interpretation of o...

  16. Genetic diversity affects testicular morphology in free-ranging lions (Panthera leo) of the Serengeti Plains and Ngorongoro Crater.

    PubMed

    Munson, L; Brown, J L; Bush, M; Packer, C; Janssen, D; Reiziss, S M; Wildt, D E

    1996-09-01

    Reduced genetic variability is known to adversely affect ejaculate quality in inbred lions (Panthera leo) physically isolated in the Ngorongoro Crater compared with outbred lions inhabiting the adjacent Serengeti Plains in East Africa. This study compared the histomorphology of testicular biopsies from these two lion populations. Ngorongoro Crater lions had fewer (P < 0.05) seminiferous tubules with spermiogenesis and fewer (P < 0.05) spermatids per seminiferous tubular cross-section than Serengeti Plains lions, although seminiferous tubular diameter did not differ (P > 0.05) between populations. Interstitial areas were greater (P < 0.05) in Crater than in Plains lions, but no qualitative differences were evident, suggesting that proportionately less testicular area was occupied by seminiferous tubules in Crater lions. None of the lions in either population had evidence of testicular degeneration. Overall results suggest that inbred Crater lions have reduced spermiogenesis and less total seminiferous tubular area per testis. These data further support the premise that genetic homogeneity compromises reproductive traits in free-living, male African lions.

  17. Genetic diversity of Vibrio parahaemolyticus strains isolated from farmed Pacific white shrimp and ambient pond water affected by acute hepatopancreatic necrosis disease outbreak in Thailand.

    PubMed

    Chonsin, Kaknokrat; Matsuda, Shigeaki; Theethakaew, Chonchanok; Kodama, Toshio; Junjhon, Jiraphan; Suzuki, Yasuhiko; Suthienkul, Orasa; Iida, Tetsuya

    2016-01-01

    Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp disease that causes massive die-offs in farmed shrimps. Recent outbreaks of AHPND in Asia have been causing great losses for shrimp culture and have become a serious socioeconomic problem. The causative agent of AHPND is Vibrio parahaemolyticus, which is typically known to cause food-borne gastroenteritis in humans. However, there have been few reports of the epidemiology of V. parahaemolyticus AHPND strains, and the genetic relationship among AHPND strains is unclear. Here, we report the genetic characterization of V. parahaemolyticus strains isolated from AHPND outbreaks in Thailand. We found eight isolates from AHPND-suspected shrimps and pond water that were positive for AHPND markers AP1 and AP2. PCR analysis confirmed that none of these eight AP-positive AHPND strains possesses the genes for the conventional virulence factors affecting to humans, such as thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH) and type III secretion system 2. Phylogenetic analysis by multilocus sequence typing showed that the AHPND strains are genetically diverse, suggesting that AHPND strains were not derived from a single genetic lineage. Our study represents the first report of molecular epidemiology of AHPND-causing V. parahaemolyticus strains using multilocus sequence typing, and provides an insight into their evolutionary mechanisms.

  18. Genetic Diversity and Human Equality.

    ERIC Educational Resources Information Center

    Dobzhansky, Theodosius

    The idea of equality often, if not frequently, bogs down in confusion and apparent contradictions; equality is confused with identity, and diversity with inequality. It would seem that the easiest way to discredit the idea of equality is to show that people are innately, genetically, and, therefore, irremediably diverse and unlike. The snare is,…

  19. Breeding and genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Corn breeding has been historically remarkably successful. Much research has investigated optimal breeding procedures, which are detailed here. A smaller effort has been put into identifying useful genetic resources for maize and how to best use them, but results from long-term base broadening effor...

  20. Genetic diversity in Trichomonas vaginalis.

    PubMed

    Meade, John C; Carlton, Jane M

    2013-09-01

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

  1. Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea

    PubMed Central

    Cortés, A J; Waeber, S; Lexer, C; Sedlacek, J; Wheeler, J A; van Kleunen, M; Bossdorf, O; Hoch, G; Rixen, C; Wipf, S; Karrenberg, S

    2014-01-01

    Current threats to biodiversity, such as climate change, are thought to alter the within-species genetic diversity among microhabitats in highly heterogeneous alpine environments. Assessing the spatial organization and dynamics of genetic diversity within species can help to predict the responses of organisms to environmental change. In this study, we evaluated whether small-scale heterogeneity in snowmelt timing restricts gene flow between microhabitats in the common long-lived dwarf shrub Salix herbacea L. We surveyed 273 genets across 12 early- and late-snowmelt sites (that is, ridges and snowbeds) in the Swiss Alps for phenological variation over 2 years and for genetic variation using seven SSR markers. Phenological differentiation triggered by differences in snowmelt timing did not correlate with genetic differentiation between microhabitats. On the contrary, extensive gene flow appeared to occur between microhabitats and slightly less extensively among adjacent mountains. However, ridges exhibited significantly lower levels of genetic diversity than snowbeds, and patterns of effective population size (Ne) and migration (Nem) between microhabitats were strongly asymmetric, with ridges acting as sources and snowbeds as sinks. As no recent genetic bottlenecks were detected in the studied sites, this asymmetry is likely to reflect current meta-population dynamics of the species dominated by gene flow via seeds rather than ancient re-colonization after the last glacial period. Overall, our results suggest that seed dispersal prevents snowmelt-driven genetic isolation, and snowbeds act as sinks of genetic diversity. We discuss the consequences of such small-scale variation in gene flow and diversity levels for population responses to climate change. PMID:24619183

  2. Local forest environment largely affects below-ground growth, clonal diversity and fine-scale spatial genetic structure in the temperate deciduous forest herb Paris quadrifolia.

    PubMed

    Jacquemyn, Hans; Brys, Rein; Honnay, Olivier; Hermy, Martin; Roldán-Ruiz, Isabel

    2005-12-01

    Paris quadrifolia (herb Paris) is a long-lived, clonal woodland herb that shows strong differences in local population size and shoot density along an environmental gradient of soil and light conditions. This environmentally based structuring may be mediated by differences in clonal growth and seedling recruitment through sexual reproduction. To study the interrelationship between environmental conditions and spatial patterns of clonal growth, the spatial genetic structure of four P. quadrifolia populations growing in strongly contrasting sites was determined. In the first place, plant excavations were performed in order to (i) determine differences in below-ground growth of genets, (ii) investigate connectedness of ramets and (iii) determine total genet size. Although no differences in internode length were found among sites, clones in moist sites were much smaller (genets usually consisted of 1-3 interconnected shoots, most of them flowering) than genets in dry sites, which consisted of up to 15 interconnected shoots, the majority of which were vegetative. Further, amplified fragment length polymorphism (AFLP) markers were used. Clonal diversity was higher in populations located in moist and productive ash-poplar forests compared to those found in drier and less productive mixed forest sites (G/N: 0.27 and 0.14 and Simpson's D: 0.84 and 0.75, respectively). Patterns of spatial population genetic structure under dry conditions revealed several large clones dominating the entire population, whereas in moist sites many small genets were observed. Nevertheless, strong spatial genetic structure of the genet population was observed. Our results clearly demonstrate that patterns of clonal diversity and growth form of P. quadrifolia differ among environments. Limited seedling recruitment and large clone sizes due to higher connectedness of ramets explain the low clonal diversity in dry sites. In moist sites, higher levels of clonal diversity and small clone sizes

  3. Genetic selection and conservation of genetic diversity*.

    PubMed

    Blackburn, H D

    2012-08-01

    For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development.

  4. Genetic diversity of Athabaskan Indians.

    PubMed

    Scott, E M

    1979-01-01

    If Athabaskan Indians are subdivided by linguistic group, a wide diversity in gene frequencies is disclosed. This diversity approximated that found when linguistically unrelated groups were compared. It was greater than that found for Eskimo-Aleus, even though the latter are more heterogeneous linguistically and subject to a wider variety of environmental conditions. Contiguity, geographic distance, and linguistic similarity were not reflected in similarity of gene frequencies. The gene found for Athabaskans appear to be the result of random process-survivor effects and genetic drift of small isolated groups. They appear to be of no value in detecting ethnic relationships.

  5. Genetic Diversity among Enterococcus faecalis

    PubMed Central

    McBride, Shonna M.; Fischetti, Vincent A.; LeBlanc, Donald J.; Moellering, Robert C.; Gilmore, Michael S.

    2007-01-01

    Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identified for their diversity and used historically for serotyping, strains that have been adapted for laboratory use, and isolates from previously described E. faecalis infection outbreaks. This collection also includes isolates first characterized as having novel plasmids, virulence traits, antibiotic resistances, and pathogenicity island (PAI) components. We evaluated variation in factors contributing to pathogenicity, including toxin production, antibiotic resistance, polymorphism in the capsule (cps) operon, pathogenicity island (PAI) gene content, and other accessory factors. This information was correlated with multi-locus sequence typing (MLST) data, which was used to define genetic lineages. Our findings show that virulence and antibiotic resistance traits can be found within many diverse lineages of E. faecalis. However, lineages have emerged that have caused infection outbreaks globally, in which several new antibiotic resistances have entered the species, and in which virulence traits have converged. Comparing genomic hybridization profiles, using a microarray, of strains identified by MLST as spanning the diversity of the species, allowed us to identify the core E. faecalis genome as consisting of an estimated 2057 unique genes. PMID:17611618

  6. Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional loss of diversity referred to as genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, ...

  7. A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s Rail (Rallus obsoletus obsoletus)

    USGS Publications Warehouse

    Wood, Dustin A.; Bui, Thuy-Vy D.; Overton, Cory T.; Vandergast, Amy; Casazza, Michael L.; Hull, Joshua M.; Takekawa, John Y.

    2016-01-01

    Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. However, we detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling in to the management regime may help evaluate population trends and guide long-term management priorities.These data support the following in-press publication: Wood, D.A., Bui, T.D., Overton, C.T., Vandergast, A.G., Casazza, M.L., Hull, J.M., and Takekawa, J.Y. Conservation Genetics (2016

  8. Genetic Diversity and Societally Important Disparities

    PubMed Central

    Rosenberg, Noah A.; Kang, Jonathan T. L.

    2015-01-01

    The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations. PMID:26354973

  9. Personalized Medicine and Human Genetic Diversity

    PubMed Central

    Lu, Yi-Fan; Goldstein, David B.; Angrist, Misha; Cavalleri, Gianpiero

    2014-01-01

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay–Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. PMID:25059740

  10. A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus)

    USGS Publications Warehouse

    Wood, Dustin A.; Bui, Thuy-Vy D.; Overton, Cory T.; Vandergast, Amy; Casazza, Michael L.; Hull, Joshua M.; Takekawa, John

    2016-01-01

    Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail (Rallus obsoletus obsoletus), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.

  11. Genetic Diversity of A-Genome Cotton.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Since Upland cotton (Gossypium hirsutum L.) is known to have relatively low levels of genetic diversity or variation in genetic makeup among individuals, a better understanding of this variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic...

  12. Extreme genetic diversity in asexual grass thrips populations.

    PubMed

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

    2016-05-01

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

  13. Genetic factors affecting dental caries risk.

    PubMed

    Opal, S; Garg, S; Jain, J; Walia, I

    2015-03-01

    This article reviews the literature on genetic aspects of dental caries and provides a framework for the rapidly changing disease model of caries. The scope is genetic aspects of various dental factors affecting dental caries. The PubMed database was searched for articles with keywords 'caries', 'genetics', 'taste', 'diet' and 'twins'. This was followed by extensive handsearching using reference lists from relevant articles. The post-genomic era will present many opportunities for improvement in oral health care but will also present a multitude of challenges. We can conclude from the literature that genes have a role to play in dental caries; however, both environmental and genetic factors have been implicated in the aetiology of caries. Additional studies will have to be conducted to replicate the findings in a different population. Identification of genetic risk factors will help screen and identify susceptible patients to better understand the contribution of genes in caries aetiopathogenesis. Information derived from these diverse studies will provide new tools to target individuals and/or populations for a more efficient and effective implementation of newer preventive measures and diagnostic and novel therapeutic approaches in the management of this disease.

  14. Synthesis and assessment of date palm genetic diversity studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A thorough assessment of genetic diversity and population differentiation of Phoenix dactylifera are critical for its dynamic conservation and sustainable utilization of its genetic diversity. Estimates of genetic diversity based on phenotypic, biochemical and molecular markers; and fruit quality tr...

  15. Evolution and genetic diversity of Theileria.

    PubMed

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

    2014-10-01

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

  16. Genetic diversity and selection in the maize starch pathway

    PubMed Central

    Whitt, Sherry R.; Wilson, Larissa M.; Tenaillon, Maud I.; Gaut, Brandon S.; Buckler, Edward S.

    2002-01-01

    Maize is both phenotypically and genetically diverse. Sequence studies generally confirm the extensive genetic variability in modern maize is consistent with a lack of selection. For more than 6,000 years, Native Americans and modern breeders have exploited the tremendous genetic diversity of maize (Zea mays ssp. mays) to create the highest yielding grain crop in the world. Nonetheless, some loci have relatively low levels of genetic variation, particularly loci that have been the target of artificial selection, like c1 and tb1. However, there is limited information on how selection may affect an agronomically important pathway for any crop. These pathways may retain the signature of artificial selection and may lack genetic variation in contrast to the rest of the genome. To evaluate the impact of selection across an agronomically important pathway, we surveyed nucleotide diversity at six major genes involved in starch metabolism and found unusually low genetic diversity and strong evidence of selection. Low diversity in these critical genes suggests that a paradigm shift may be required for future maize breeding. Rather than relying solely on the diversity within maize or on transgenics, future maize breeding would perhaps benefit from the incorporation of alleles from maize's wild relatives. PMID:12244216

  17. Implications of recurrent disturbance for genetic diversity.

    PubMed

    Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

    2016-02-01

    Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

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

    PubMed Central

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

    2016-01-01

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

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

    PubMed

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

    2016-02-10

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

  20. Genetic Structure and Potential Environmental Determinants of Local Genetic Diversity in Japanese Honeybees (Apis cerana japonica)

    PubMed Central

    Nagamitsu, Teruyoshi; Yasuda, Mika; Saito-Morooka, Fuki; Inoue, Maki N.; Nishiyama, Mio; Goka, Koichi; Sugiura, Shinji; Maeto, Kaoru; Okabe, Kimiko; Taki, Hisatomo

    2016-01-01

    Declines in honeybee populations have been a recent concern. Although causes of the declines remain unclear, environmental factors may be responsible. We focused on the potential environmental determinants of local populations of wild honeybees, Apis cerana japonica, in Japan. This subspecies has little genetic variation in terms of its mitochondrial DNA sequences, and genetic variations at nuclear loci are as yet unknown. We estimated the genetic structure and environmental determinants of local genetic diversity in nuclear microsatellite genotypes of fathers and mothers, inferred from workers collected at 139 sites. The genotypes of fathers and mothers showed weak isolation by distance and negligible genetic structure. The local genetic diversity was high in central Japan, decreasing toward the peripheries, and depended on the climate and land use characteristics of the sites. The local genetic diversity decreased as the annual precipitation increased, and increased as the proportion of urban and paddy field areas increased. Positive effects of natural forest area, which have also been observed in terms of forager abundance in farms, were not detected with respect to the local genetic diversity. The findings suggest that A. cerana japonica forms a single population connected by gene flow in its main distributional range, and that climate and landscape properties potentially affect its local genetic diversity. PMID:27898704

  1. Diversity of potato genetic resources

    PubMed Central

    Machida-Hirano, Ryoko

    2015-01-01

    A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection. PMID:25931978

  2. Molecular phylogeny and genetic diversity of Lygus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inter- and intraspecific genetic diversity in North American Lygus was using nuclear and mitochondrial DNA. DNA sequences have been obtained from the mitochondrial cox1 and cox2 genes, the nuclear ITS1 spacer, and regions flanking microsatellites (MSFR). The Fargo lab sequenced a region overlapp...

  3. Genetic Diversity of Natural Crossing in Cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have shown previously genetic diversity in mature cotton pollen sensitivity to low humidity. This study investigated the impact of pollen sensitivity to low humidity on the amount of outcrossing to neighboring plants. We utilized “red” and “green” pigmented cotton, in addition to gossypol glan...

  4. Accessing genetic diversity for crop improvement.

    PubMed

    Glaszmann, J C; Kilian, B; Upadhyaya, H D; Varshney, R K

    2010-04-01

    Vast germplasm collections are accessible but their use for crop improvement is limited-efficiently accessing genetic diversity is still a challenge. Molecular markers have clarified the structure of genetic diversity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of 'core reference sets' so as to facilitate material sharing within the scientific community.

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

    PubMed

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

    2014-02-01

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

  6. Genetic diversity of Ascaris in southwestern Uganda.

    PubMed

    Betson, Martha; Nejsum, Peter; Llewellyn-Hughes, Julia; Griffin, Claire; Atuhaire, Aaron; Arinaitwe, Moses; Adriko, Moses; Ruggiana, Andrew; Turyakira, Grace; Kabatereine, Narcis B; Stothard, J Russell

    2012-02-01

    Despite the common occurrence of ascariasis in southwestern Uganda, helminth control in the region has been limited. To gain further insights into the genetic diversity of Ascaris in this area, a parasitological survey in mothers (n=41) and children (n=74) living in two villages, Habutobere and Musezero, was carried out. Adult Ascaris worms were collected from infected individuals by chemo-expulsion using pyrantel pamoate treatment. Genetic diversity within these worms was assessed by inspection of DNA sequence variation in a mitochondrial marker and length polymorphism at microsatellite loci. Overall prevalence of ascariasis was 42.5% in mothers and 30.4% in their children and a total of 98 worms was examined from 18 hosts. Sequence analysis of a portion of the mitochondrial cytochrome c oxidase subunit 1 gene revealed 19 different haplotypes, 13 of which had not been previously encountered. Microsatellite analysis using eight loci provided evidence for high gene flow between worm populations from the two villages but comparing these worms with others obtained in a prior study on Unguja, Zanzibar, confirmed little genetic exchange and mixing of worm populations between the two areas. By adding to our understanding of the genetic diversity of Ascaris in Africa, this study provides useful information for monitoring changes in parasite population structure in the face of ongoing and future control.

  7. Inbreeding levels in swine: Ramifications for Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Globally, genetic diversity of livestock populations is contracting. Knowing the true extent of the contraction is needed to develop effective conservation strategies. While contractions of genetic diversity have been documented at the breed level, little within breed documentation has occurred. ...

  8. Mapping human genetic diversity in Asia.

    PubMed

    Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Cutiongco-de la Paz, Eva Maria C; De Ungria, Maria Corazon A; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi

    2009-12-11

    Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

  9. Global genetic diversity of Aedes aegypti.

    PubMed

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

    2016-11-01

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

  10. Molecular genetics in affective illness

    SciTech Connect

    Mendlewicz, J.; Sevy, S.; Mendelbaum, K. )

    1993-01-01

    Genetic transmission in manic depressive illness (MDI) has been explored in twins, adoption, association, and linkage studies. The X-linked transmission hypothesis has been tested by using several markers on chromosome X: Xg blood group, color blindness, glucose-6-phosphate dehydrogenase (G6PD), factor IX (hemophilia B), and DNA probes such as DXS15, DXS52, F8C, ST14. The hypothesis of autosomal transmission has been tested by association studies with the O blood group located on chromosome 9, as well as linkage studies on chromosome 6 with the Human Leucocyte Antigens (HLA) haplotypes and on Chromosome 11 with DNA markers for the following genes: D2 dopamine receptor, tyrosinase, C-Harvey-Ras-A (HRAS) oncogene, insuline (ins), and tyrosine hydroxylase (TH). Although linkage studies support the hypothesis of a major locus for the transmission of MDI in the Xq27-28 region, several factors are limiting the results, and are discussed in the present review. 105 refs., 1 fig., 2 tabs.

  11. Genetic diversity of koala retroviral envelopes.

    PubMed

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

    2015-03-17

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

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

    PubMed

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

    2014-01-01

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

  13. Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod.

    PubMed

    Bach, Lis; Dahllöf, Ingela

    2012-06-15

    The objective of this study was to investigate whether populations inhabiting a contaminated environment are affected in terms of decreased genetic diversity due to selection of tolerant genotypes and if such effect carries a cost. Marine arctic amphipod populations (Orchomenella pinguis) were collected from sites within a contaminated fjord, as well as from sites outside the fjord on the west-coast of Greenland over three years (2006-2008). Impacts on genetic diversity, effects on resilience such as development of tolerance and cost were determined. AFLP-analysis was used to explore within and between population genetic diversity, and exposure studies were performed where the populations were subjected to known and unknown stressors to assess resilience. Populations collected at three contaminated sites all had reduced genetic diversity in 2007 compared to populations outside the fjord. This pattern was different in 2008 as all contaminated site populations increased in diversity, whereas a decrease in diversity occurred at the outer sites. However, tolerance, but even more so, cost, was related to contamination exposure in 2008, in spite of the shift in genetic diversity. We suggest that contamination rapidly induces effects that can be captured as tolerance and associated cost, whereas effects on genetic diversity can be difficult to separate from recent migration events that dilute eventual decreases in diversity due to contamination pressure. As long as impacted populations can be influenced by migration events that increase the genetic diversity and add health to an affected population, populations in contaminated areas may have enhanced probability of survival.

  14. Turtle Carapace Anomalies: The Roles of Genetic Diversity and Environment

    PubMed Central

    Velo-Antón, Guillermo; Becker, C. Guilherme; Cordero-Rivera, Adolfo

    2011-01-01

    Background Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. Methodology/Principal Findings In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. Conclusions/Significance Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations. PMID:21533278

  15. Genetic diversity of Ehrlichia canis in Brazil.

    PubMed

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

    2013-06-28

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

  16. Arenavirus genetic diversity and its biological implications.

    PubMed

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

    2009-07-01

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

  17. The silent threat of low genetic diversity

    USGS Publications Warehouse

    Hunter, Margaret E.

    2013-01-01

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

  18. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    PubMed

    Rueppell, Olav; Meier, Stephen; Deutsch, Roland

    2012-01-01

    Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  19. Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China.

    PubMed

    Huang, Wenda; Zhao, Xueyong; Zhao, Xin; Li, Yulin; Lian, Jie

    2016-11-01

    Caragana microphylla (Leguminosae) is a dominant climax semishrub species in northern China. We evaluated genetic variation within and among populations sampled from three different environmental gradients in Horqin Sandy Land in northern China using intersimple sequence repeats markers and investigated the possible existence of relationships between genetic diversity and environmental factors. The results showed that C. microphylla have high genetic diversity, and environmental gradients affected genetic diversity of C. microphylla populations. Genetic diversity of all populations was affected by many environmental factors and as well correlated with warm index and soil Olsen phosphorus (SOP) concentration. These results have important implications for restoration and management of these degraded ecosystems in arid and semi-arid areas.

  20. Rarity and genetic diversity in Indo–Pacific Acropora corals

    PubMed Central

    Richards, Zoe T; Oppen, Madeleine J H

    2012-01-01

    Among various potential consequences of rarity is genetic erosion. Neutral genetic theory predicts that rare species will have lower genetic diversity than common species. To examine the association between genetic diversity and rarity, variation at eight DNA microsatellite markers was documented for 14 Acropora species that display different patterns of distribution and abundance in the Indo–Pacific Ocean. Our results show that the relationship between rarity and genetic diversity is not a positive linear association because, contrary to expectations, some rare species are genetically diverse and some populations of common species are genetically depleted. Our data suggest that inbreeding is the most likely mechanism of genetic depletion in both rare and common corals, and that hybridization is the most likely explanation for higher than expected levels of genetic diversity in rare species. A significant hypothesis generated from our study with direct conservation implications is that as a group, Acropora corals have lower genetic diversity at neutral microsatellite loci than may be expected from their taxonomic diversity, and this may suggest a heightened susceptibility to environmental change. This hypothesis requires validation based on genetic diversity estimates derived from a large portion of the genome. PMID:22957189

  1. DEVELOPMENT OF DNA BASED MICROSATELLITE MARKER TECHNOLOGY FOR STUDIES OF GENETIC DIVERSITY IN CENTRAL STONEROLLER (CAMPOSTOMA ANOMALUM) POPULATIONS

    EPA Science Inventory

    The level of genetic diversity of aquatic species is a critical indicator of stream system condition for which few data exist. There is strong evidence suggesting that environmental stressors affect the genetic diversity of exposed populations. In order to study genetic diversi...

  2. Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

    PubMed

    Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

  3. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    USGS Publications Warehouse

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  4. High genetic diversity is not essential for successful introduction.

    PubMed

    Rollins, Lee A; Moles, Angela T; Lam, Serena; Buitenwerf, Robert; Buswell, Joanna M; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B

    2013-11-01

    Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.

  5. High genetic diversity is not essential for successful introduction

    PubMed Central

    Rollins, Lee A; Moles, Angela T; Lam, Serena; Buitenwerf, Robert; Buswell, Joanna M; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B

    2013-01-01

    Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive. PMID:24340190

  6. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    PubMed

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  7. Genetic diversity increases insect herbivory on oak saplings.

    PubMed

    Castagneyrol, Bastien; Lagache, Lélia; Giffard, Brice; Kremer, Antoine; Jactel, Hervé

    2012-01-01

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

  8. Effects of inbreeding on the genetic diversity of populations.

    PubMed Central

    Charlesworth, Deborah

    2003-01-01

    The study of variability within species is important to all biologists who use genetic markers. Since the discovery of molecular variability among normal individuals, data have been collected from a wide range of organisms, and it is important to understand the major factors affecting diversity levels and patterns. Comparisons of inbreeding and outcrossing populations can contribute to this understanding, and therefore studying plant populations is important, because related species often have different breeding systems. DNA sequence data are now starting to become available from suitable plant and animal populations, to measure and compare variability levels and test predictions. PMID:12831472

  9. Genetic diversity in Sargasso Sea bacterioplankton.

    PubMed

    Giovannoni, S J; Britschgi, T B; Moyer, C L; Field, K G

    1990-05-03

    Bacterioplankton are recognized as important agents of biogeochemical change in marine ecosystems, yet relatively little is known about the species that make up these communities. Uncertainties about the genetic structure and diversity of natural bacterioplankton populations stem from the traditional difficulties associated with microbial cultivation techniques. Discrepancies between direct counts and plate counts are typically several orders of magnitude, raising doubts as to whether cultivated marine bacteria are actually representative of dominant planktonic species. We have phylogenetically analysed clone libraries of eubacterial 16S ribosomal RNA genes amplified from natural populations of Sargasso Sea picoplankton by the polymerase chain reaction. The analysis indicates the presence of a novel microbial group, the SAR11 cluster, which appears to be a significant component of this oligotrophic bacterioplankton community. A second cluster of lineages related to the oxygenic phototrophs--cyanobacteria, prochlorophytes and chloroplasts--was also observed. However, none of the genes matched the small subunit rRNA sequences of cultivated marine cyanobacteria from similar habitats. The diversity of 16S rRNA genes observed within the clusters suggests that these bacterioplankton may be consortia of independent lineages sharing surprisingly distant common ancestors.

  10. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    PubMed Central

    Young, Carolyn A.; Schardl, Christopher L.; Panaccione, Daniel G.; Florea, Simona; Takach, Johanna E.; Charlton, Nikki D.; Moore, Neil; Webb, Jennifer S.; Jaromczyk, Jolanta

    2015-01-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294

  11. Genetic diversity among Lassa virus strains.

    PubMed

    Bowen, M D; Rollin, P E; Ksiazek, T G; Hustad, H L; Bausch, D G; Demby, A H; Bajani, M D; Peters, C J; Nichol, S T

    2000-08-01

    The arenavirus Lassa virus causes Lassa fever, a viral hemorrhagic fever that is endemic in the countries of Nigeria, Sierra Leone, Liberia, and Guinea and perhaps elsewhere in West Africa. To determine the degree of genetic diversity among Lassa virus strains, partial nucleoprotein (NP) gene sequences were obtained from 54 strains and analyzed. Phylogenetic analyses showed that Lassa viruses comprise four lineages, three of which are found in Nigeria and the fourth in Guinea, Liberia, and Sierra Leone. Overall strain variation in the partial NP gene sequence was found to be as high as 27% at the nucleotide level and 15% at the amino acid level. Genetic distance among Lassa strains was found to correlate with geographic distance rather than time, and no evidence of a "molecular clock" was found. A method for amplifying and cloning full-length arenavirus S RNAs was developed and used to obtain the complete NP and glycoprotein gene (GP1 and GP2) sequences for two representative Nigerian strains of Lassa virus. Comparison of full-length gene sequences for four Lassa virus strains representing the four lineages showed that the NP gene (up to 23.8% nucleotide difference and 12.0% amino acid difference) is more variable than the glycoprotein genes. Although the evolutionary order of descent within Lassa virus strains was not completely resolved, the phylogenetic analyses of full-length NP, GP1, and GP2 gene sequences suggested that Nigerian strains of Lassa virus were ancestral to strains from Guinea, Liberia, and Sierra Leone. Compared to the New World arenaviruses, Lassa and the other Old World arenaviruses have either undergone a shorter period of diverisification or are evolving at a slower rate. This study represents the first large-scale examination of Lassa virus genetic variation.

  12. Genetic calibration of species diversity among North America's freshwater fishes

    PubMed Central

    April, Julien; Mayden, Richard L.; Hanner, Robert H.; Bernatchez, Louis

    2011-01-01

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required. PMID:21670289

  13. Genetic calibration of species diversity among North America's freshwater fishes.

    PubMed

    April, Julien; Mayden, Richard L; Hanner, Robert H; Bernatchez, Louis

    2011-06-28

    Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

  14. Does genetic diversity limit disease spread in natural host populations?

    PubMed Central

    King, K C; Lively, C M

    2012-01-01

    It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding ‘diversity thresholds.' PMID:22713998

  15. Affective Education for Gifted, Culturally Diverse Learners

    ERIC Educational Resources Information Center

    Baldwin, Alexinia

    2009-01-01

    Over the years, there has been an ongoing controversy about affective education. Some see it as an important element of good teaching, and some see it as fluff, diminishing academics, and playing into the "feel good" movement. While criticisms may be appropriate in some situations, affective education can play a fundamental role in other…

  16. The impact of recent events on human genetic diversity

    PubMed Central

    Jobling, Mark A.

    2012-01-01

    The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics. PMID:22312046

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

    USGS Publications Warehouse

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

    2011-01-01

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

  18. Comparison of Genetic Diversity Between US and Kazak Sheep Breeds.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To secure US genetic diversity it is beneficial to compare US and non-US breeds. Such information may also be used to identify areas of sampling for diverse genetic resources. Kazakhstan (KZ) provides an interesting comparison due to its history of sheep production and proximity to the Silk Route, w...

  19. Status of genetic diversity of U. S. dairy goat breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity underpins the livestock breeders’ ability to improve the production potential of their livestock. Therefore, it is important to periodically assess genetic diversity within a breed. Such an analysis was conducted on U.S. dairy goat breeds and this article is an overview of that wo...

  20. Status of genetic diversity of U. S. dairy goat breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity underpins the livestock breeders’ ability to improve the production potential of their livestock. Therefore, it is important to periodically assess genetic diversity within a breed. Such an analysis was conducted on U.S. dairy goat breeds: Alpine, LaMancha, Nigerian Dwarf, Nubian, ...

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

    PubMed

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

    2016-04-01

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

  2. Genetic diversity of Echinococcus spp. in Russia.

    PubMed

    Konyaev, Sergey V; Yanagida, Tetsuya; Nakao, Minoru; Ingovatova, Galina M; Shoykhet, Yakov N; Bondarev, Alexandr Y; Odnokurtsev, Valeriy A; Loskutova, Kyunnyay S; Lukmanova, Gulnur I; Dokuchaev, Nikolai E; Spiridonov, Sergey; Alshinecky, Mikhail V; Sivkova, Tatyana N; Andreyanov, Oleg N; Abramov, Sergey A; Krivopalov, Anton V; Karpenko, Sergey V; Lopatina, Natalia V; Dupal, Tamara A; Sako, Yasuhito; Ito, Akira

    2013-11-01

    In Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus.

  3. Genetic Diversity of Salt Tolerance in Miscanthus

    PubMed Central

    Chen, Chang-Lin; van der Schoot, Hanneke; Dehghan, Shiva; Alvim Kamei, Claire L.; Schwarz, Kai-Uwe; Meyer, Heike; Visser, Richard G. F.; van der Linden, C. Gerard

    2017-01-01

    Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered mechanisms and traits that can be used to improve the yield under salt stress. Seventy genotypes of Miscanthus (including 57 M. sinensis, 5 M. sacchariflorus, and 8 hybrids) were evaluated for salt tolerance under saline (150 mM NaCl) and normal growing conditions using a hydroponic system. Analyses of shoot growth traits and ion concentrations revealed the existence of large variation for salt tolerance in the genotypes. We identified genotypes with potential for high biomass production both under control and saline conditions that may be utilized for growth under marginal, saline conditions. Several relatively salt tolerant genotypes had clearly lower Na+ concentrations and showed relatively high K+/Na+ ratios in the shoots under salt stress, indicating that a Na+ exclusion mechanism was utilized to prevent Na+ accumulation in the leaves. Other genotypes showed limited reduction in leaf expansion and growth rate under saline conditions, which may be indicative of osmotic stress tolerance. The genotypes demonstrating potentially different salt tolerance mechanisms can serve as starting material for breeding programs aimed at improving salinity tolerance of Miscanthus. PMID:28261243

  4. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

    PubMed

    Osborne, Megan J; Perkin, Joshuah S; Gido, Keith B; Turner, Thomas F

    2014-12-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic-spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most tributary basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and in response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage.

  5. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes

    PubMed Central

    Osborne, Megan J; Perkin, Joshuah S.; Gido, Keith B.; Turner, Thomas F.

    2014-01-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits, and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model, and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. PMID:25327780

  6. Multiple paternity does not depend on male genetic diversity.

    PubMed

    Thonhauser, Kerstin E; Raveh, Shirley; Penn, Dustin J

    2014-07-01

    Polyandry is common in many species and it has been suggested that females engage in multiple mating to increase the genetic diversity of their offspring (genetic diversity hypothesis). Multiple paternity occurs in 30% of litters in wild populations of house mice, Mus musculus musculus, and multiple-sired litters are genetically more diverse than single-sired ones. Here, we aimed to test whether female house mice produce multiple-sired litters when they have the opportunity to produce genetically diverse litters. We assessed the rates of multiple paternity when females could choose to mate with two males that were genetically dissimilar to each other (i.e. nonsiblings and MHC dissimilar) compared with when females could choose to mate with two males that were genetically similar to each other (i.e. siblings and shared MHC alleles). Multiple mating may depend upon a female's own condition, and, therefore, we also tested whether inbred (from full-sibling matings) females were more likely to produce multiple-sired progeny than outbred controls. Overall we found that 29% of litters had multiple sires, but we found no evidence that females were more likely to produce multiple-sired litters when they had the opportunity to mate with genetically dissimilar males compared with controls, regardless of whether females were inbred or outbred. Thus, our findings do not support the idea that female mice increase multiple paternity when they have the opportunity to increase the genetic diversity of their offspring, as expected from the genetic diversity hypothesis.

  7. The population genetics of mimetic diversity in Heliconius butterflies

    PubMed Central

    Kronforst, Marcus R; Gilbert, Lawrence E

    2007-01-01

    Theory predicts strong stabilizing selection on warning patterns within species and convergent evolution among species in Müllerian mimicry systems yet Heliconius butterflies exhibit extreme wing pattern diversity. One potential explanation for the evolution of this diversity is that genetic drift occasionally allows novel warning patterns to reach the frequency threshold at which they gain protection. This idea is controversial, however, because Heliconius butterflies are unlikely to experience pronounced population subdivision and local genetic drift. To examine the fine-scale population genetic structure of Heliconius butterflies we genotyped 316 individuals from eight Costa Rican Heliconius species with 1428 AFLP markers. Six species exhibited evidence of population subdivision and/or isolation by distance indicating genetic differentiation among populations. Across species, variation in the extent of local genetic drift correlated with the roles different species have played in generating pattern diversity: species that originally generated the diversity of warning patterns exhibited striking population subdivision while species that later radiated onto these patterns had intermediate levels of genetic diversity and less genetic differentiation among populations. These data reveal that Heliconius butterflies possess the coarse population genetic structure necessary for local populations to experience pronounced genetic drift which, in turn, could explain the origin of mimetic diversity. PMID:18077248

  8. Diversity and general student scholarship recipient essays: 2010 National Society of Genetic Counselors Membership Committee.

    PubMed

    Liu, Tina; Patek, Kyla; Schneider, Kami Wolfe

    2011-12-01

    In an effort to increase the diversity of the membership of the National Society of Genetic Counselors (NSGC), the Membership Committee provided two $500 scholarships to genetic counseling students planning to attend the NSGC AEC meeting in Dallas, Texas in October 2010. Requirements for applicants of both scholarships included enrollment in the fall of 2010, good standing at an accredited genetic counseling training program, and NSGC membership or plans to join in 2011. Students who are from communities underrepresented in the NSGC, including, but not limited to, those of minority cultural/ethnic backgrounds and those with disabilities were eligible to apply for the "Diversity" scholarship. Students from all backgrounds who have an interest in diversity issues were eligible to apply for the "General" scholarship. Applicants wrote essays 1000 words or less answering the following questions: How has your identity as a member of a group underrepresented in the genetic counseling profession affected your pursuit of this career? What do you feel is lacking in genetic counseling to address the issues of underrepresented groups? What strategies do you recommend for addressing these issues and/or increasing diversity? Why do you think diversity is an important issue for the field of genetic counseling? What strategies do you recommend to attract and retain students, especially those from underrepresented populations, into the field of genetic counseling? How do you envision contributing to these strategies? The essays by the award recipients elucidated interesting perspectives and ideas for increasing diversity in the genetic counseling profession.

  9. Historical habitat connectivity affects current genetic structure in a grassland species.

    PubMed

    Münzbergová, Z; Cousins, S A O; Herben, T; Plačková, I; Mildén, M; Ehrlén, J

    2013-01-01

    Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co-dominant markers to estimate genetic diversity and deviation from Hardy-Weinberg equilibrium in 31 populations distributed within a 5 km(2) agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale.

  10. Network Diversity and Affect Dynamics: The Role of Personality Traits

    PubMed Central

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2016-01-01

    People divide their time unequally among their social contacts due to time constraints and varying strength of relationships. It was found that high diversity of social communication, dividing time more evenly among social contacts, is correlated with economic well-being both at macro and micro levels. Besides economic well-being, it is not clear how the diversity of social communication is also associated with the two components of individuals’ subjective well-being, positive and negative affect. Specifically, positive affect and negative affect are two independent dimensions representing the experience (feeling) of emotions. In this paper, we investigate the relationship between the daily diversity of social communication and dynamic affect states that people experience in their daily lives. We collected two high-resolution datasets that capture affect scores via daily experience sampling surveys and social interaction through wearable sensing technologies: sociometric badges for face-to-face interaction and smart phones for mobile phone calls. We found that communication diversity correlates with desirable affect states–e.g. an increase in the positive affect state or a decrease in the negative affect state–for some personality types, but correlates with undesirable affect states for others. For example, diversity in phone calls is experienced as good by introverts, but bad by extroverts; diversity in face-to-face interaction is experienced as good by people who tend to be positive by nature (trait) but bad for people who tend to be not positive by nature. More broadly, the moderating effect of personality type on the relationship between diversity and affect was detected without any knowledge of the type of social tie or the content of communication. This provides further support for the power of unobtrusive sensing in understanding social dynamics, and in measuring the effect of potential interventions designed to improve well-being. PMID:27035904

  11. Network Diversity and Affect Dynamics: The Role of Personality Traits.

    PubMed

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2016-01-01

    People divide their time unequally among their social contacts due to time constraints and varying strength of relationships. It was found that high diversity of social communication, dividing time more evenly among social contacts, is correlated with economic well-being both at macro and micro levels. Besides economic well-being, it is not clear how the diversity of social communication is also associated with the two components of individuals' subjective well-being, positive and negative affect. Specifically, positive affect and negative affect are two independent dimensions representing the experience (feeling) of emotions. In this paper, we investigate the relationship between the daily diversity of social communication and dynamic affect states that people experience in their daily lives. We collected two high-resolution datasets that capture affect scores via daily experience sampling surveys and social interaction through wearable sensing technologies: sociometric badges for face-to-face interaction and smart phones for mobile phone calls. We found that communication diversity correlates with desirable affect states--e.g. an increase in the positive affect state or a decrease in the negative affect state--for some personality types, but correlates with undesirable affect states for others. For example, diversity in phone calls is experienced as good by introverts, but bad by extroverts; diversity in face-to-face interaction is experienced as good by people who tend to be positive by nature (trait) but bad for people who tend to be not positive by nature. More broadly, the moderating effect of personality type on the relationship between diversity and affect was detected without any knowledge of the type of social tie or the content of communication. This provides further support for the power of unobtrusive sensing in understanding social dynamics, and in measuring the effect of potential interventions designed to improve well-being.

  12. Does natural variation in diversity affect biotic resistance?

    USGS Publications Warehouse

    Harrison, Susan; Cornell, Howard; Grace, James B.

    2015-01-01

    Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

  13. Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax

    PubMed Central

    Friedrich, Lindsey R.; Popovici, Jean; Kim, Saorin; Dysoley, Lek; Zimmerman, Peter A.; Menard, Didier; Serre, David

    2016-01-01

    Background Plasmodium vivax is the most widely distributed human malaria parasite with 2.9 billion people living in endemic areas. Despite intensive malaria control efforts, the proportion of cases attributed to P. vivax is increasing in many countries. Genetic analyses of the parasite population and its dynamics could provide an assessment of the efficacy of control efforts, but, unfortunately, these studies are limited in P. vivax by the lack of informative markers and high-throughput genotyping methods. Methodology/Principal Findings We developed a sequencing-based assay to simultaneously genotype more than 100 SNPs and applied this approach to ~500 P. vivax-infected individuals recruited across nine locations in Cambodia between 2004 and 2013. Our analyses showed that the vast majority of infections are polyclonal (92%) and that P. vivax displays high genetic diversity in Cambodia without apparent geographic stratification. Interestingly, our analyses also revealed that the proportion of monoclonal infections significantly increased between 2004 and 2013, possibly suggesting that malaria control strategies in Cambodia may be successfully affecting the parasite population. Conclusions/Significance Our findings demonstrate that this high-throughput genotyping assay is efficient in characterizing P. vivax diversity and can provide valuable insights to assess the efficacy of malaria elimination programs or to monitor the spread of specific parasites. PMID:27018585

  14. [Molecular genetic diversity of Fujian domestic duck breeds].

    PubMed

    Li, Hui-fang; Li, Bi-chun; Ma, Yue-hui; Tang, Qing-ping; Chen, Kuan-wei; Tu, Yun-jie

    2007-02-01

    By using 28 micro-satellite markers with better polymorphism, this paper studied the genetic diversity of four Fujian provincial domestic duck breeds Jinding, Putian black, Liancheng white, and Shanma. According to the alleles frequencies, the polymorphic information content, average heterozygosity, anaqular genetic distance (DA) and Nei' s standard genetic distance (DS) for each breed were calculated. Based on DA and DS, four dendrograms were obtained by neighbor-joining (NJ) and UPGMA methods. The results showed that the average heterozygosity of the four duck breeds was 0. 5353, indicating that the protection of the genetic diversity of these breeds should be strengthened. The orders of the two types of genetic distances among the breeds were accordant, and the dendrograms were the same, reflecting that much more micro-satellite loci should be adopted to obtain more universal conclusions when the genetic diversity was analyzed. The phylogenetic relationships among the four duck breeds were in accordance with their economic types and ecological localities.

  15. Surviving with low genetic diversity: the case of albatrosses.

    PubMed

    Milot, Emmanuel; Weimerskirch, Henri; Duchesne, Pierre; Bernatchez, Louis

    2007-03-22

    Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses (Diomedea exulans and Diomedea amsterdamensis) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Divergence time of the two species is estimated at 0.84 Myr ago from cytochrome b data. We tested the hypothesis that both albatrosses inherited poor genetic diversity from their common ancestor. Within the wandering albatross, per cent polymorphic loci and expected heterozygosity at amplified fragment length polymorphisms were approximately one-third of the minimal values reported in other vertebrates. Genetic diversity in the Amsterdam albatross, which is recovering from a severe bottleneck, was about twice as low as in the wandering albatross. Simulations supported the hypothesis that genetic diversity in albatrosses was already depleted prior to their divergence. Given the generally high breeding success of these species, it is likely that they are not suffering much from their impoverished diversity. Whether albatrosses are unique in this regard is unknown, but they appear to challenge the classical view about the negative consequences of genetic depletion on species survival.

  16. Surviving with low genetic diversity: the case of albatrosses

    PubMed Central

    Milot, Emmanuel; Weimerskirch, Henri; Duchesne, Pierre; Bernatchez, Louis

    2007-01-01

    Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses (Diomedea exulans and Diomedea amsterdamensis) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Divergence time of the two species is estimated at 0.84 Myr ago from cytochrome b data. We tested the hypothesis that both albatrosses inherited poor genetic diversity from their common ancestor. Within the wandering albatross, per cent polymorphic loci and expected heterozygosity at amplified fragment length polymorphisms were approximately one-third of the minimal values reported in other vertebrates. Genetic diversity in the Amsterdam albatross, which is recovering from a severe bottleneck, was about twice as low as in the wandering albatross. Simulations supported the hypothesis that genetic diversity in albatrosses was already depleted prior to their divergence. Given the generally high breeding success of these species, it is likely that they are not suffering much from their impoverished diversity. Whether albatrosses are unique in this regard is unknown, but they appear to challenge the classical view about the negative consequences of genetic depletion on species survival. PMID:17251114

  17. The relative importance of host-plant genetic diversity in structuring the associated herbivore community.

    PubMed

    Tack, Ayco J M; Roslin, Tomas

    2011-08-01

    Recent studies suggest that intraspecific genetic diversity in one species may leave a substantial imprint on the surrounding community and ecosystem. Here, we test the hypothesis that genetic diversity within host-plant patches translates into consistent and ecologically important changes in the associated herbivore community. More specifically, we use potted, grafted oak saplings to construct 41 patches of four saplings each, with one, two, or four tree genotypes represented among the host plants. These patches were divided among two common gardens. Focusing first at the level of individual trees, we assess how tree-specific genotypic identity, patch-level genetic diversity, garden-level environmental variation, and their interactions affect the structure of the herbivore community. At the level of host-plant patches, we analyze whether the joint responses of herbivore species to environmental variation and genetic diversity result in differences in species diversity among tree quartets. Strikingly, both species-specific abundances and species diversity varied substantially among host-tree genotypes, among common gardens, and among specific locations within individual gardens. In contrast, the genetic diversity of the patch left a detectable imprint on local abundances of only two herbivore taxa. In both cases, the effect of genetic diversity was inconsistent among gardens and among host-plant genotypes. While the insect community differed significantly among individual host-plant genotypes, there were no interactive effects of the number of different genotypes within the patch. Overall, additive effects of intraspecific genetic diversity of the host plant explained a similar or lower proportion (7-10%) of variation in herbivore species diversity than did variation among common gardens. Combined with the few previous studies published to date, our study suggests that the impact of host-plant genetic diversity on the herbivore community can range from none to

  18. Demographic events and evolutionary forces shaping European genetic diversity.

    PubMed

    Veeramah, Krishna R; Novembre, John

    2014-07-24

    Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.

  19. Demographic Events and Evolutionary Forces Shaping European Genetic Diversity

    PubMed Central

    Veeramah, Krishna R.; Novembre, John

    2014-01-01

    Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease. PMID:25059709

  20. Genetic diversity and structure in two protected Posidonia oceanica meadows.

    PubMed

    Micheli, Carla; D'Esposito, Daniela; Belmonte, Alessandro; Peirano, Andrea; Valiante, Luigi Maria; Procaccini, Gabriele

    2015-08-01

    Posidonia oceanica meadows growing along the west Mediterranean coastline are under continuous anthropogenic pressure. The way meadow health correlates with genetic and genotypic diversity in P. oceanica, is still under debate. Here we report a microsatellite analysis of two P. oceanica meadows living in protected areas of the Ligurian (Monterosso al Mare, MPA of "Cinque Terre") and central Tyrrhenian Sea (Santa Marinella, regional Site of Community Importance). Both meadows were recently classified as "disturbed", according to shoot density and other phenological parameters. Between the two meadows, Santa Marinella showed higher genetic diversity, while clear genetic substructure was present in both sites, reflecting high spatial heterogeneity. The present study suggests that genetic diversity does not match unequivocally with shoot density and leaf morphology and that small scale intra-meadow heterogeneity is an important factor to consider for establishing the relation between genetic/genotypic variability and health of natural seagrass meadows.

  1. Genetic structure and diversity of animal populations exposed to metal pollution.

    PubMed

    Mussali-Galante, Patricia; Tovar-Sánchez, Efraín; Valverde, Mahara; Rojas, Emilio

    2014-01-01

    Studying the genetic diversity of wild populations that are affected by pollution provides a basis for estimating the risks of environmental contamination to both wildlife, and indirectly to humans. Such research strives to produce both a better understanding of the underlying mechanisms by which genetic diversity is affected,and the long-term effects of the pollutants involved.In this review, we summarize key aspects of the field of genetic ecotoxicology that encompasses using genetic patterns to examine metal pollutants as environmental stressors of natural animal populations. We address genetic changes that result from xenobiotic exposure versus genetic alterations that result from natural ecological processes. We also describe the relationship between metal exposure and changes in the genetic diversity of chronically exposed populations, and how the affected populations respond to environmental stress. Further, we assess the genetic diversity of animal populations that were exposed to metals, focusing on the literature that has been published since the year 2000.Our review disclosed that the most common metals found in aquatic and terrestrial ecosystems were Cd, Zn, Cu and Pb; however, differences in the occurrence between aquatic (Cd=Zn>Cu>Pb>Hg) and terrestrial (Cu>Cd>Pb>Zn>Ni)environments were observed. Several molecular markers were used to assess genetic diversity in impacted populations, the order of the most common ones of which were SSR's > allozyme > RAPD's > mtDNA sequencing> other molecular markers.Genetic diversity was reduced for nearly all animal populations that were exposed to a single metal, or a mixture of metals in aquatic ecosystems (except in Hyalella azteca, Littorina littorea, Salmo trutta, and Gobio gobio); however, the pattern was less clear when terrestrial ecosystems were analyzed.We propose that future research in the topic area of this paper emphasizes seven key areas of activity that pertain to the methodological design of genetic

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-12-01

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

  4. Understanding Genetic Diversity of Sorghum Using Quantitative Traits

    PubMed Central

    Sinha, Sweta; Kumaravadivel, N.

    2016-01-01

    Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement. PMID:27382499

  5. Accumulation of genetic diversity in the US Potato Genebank

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Impact of genetic variation on synaptic protein levels in genetically diverse mice.

    PubMed

    Loos, Maarten; Li, Ka Wan; van der Schors, Roel; Gouwenberg, Yvonne; van der Loo, Rolinka; Williams, Robert W; Smit, August B; Spijker, Sabine

    2016-04-01

    The relative abundance of synaptic proteins shapes protein complex formation and is essential for synapse function and behavioral fitness. Here, we have used a panel of highly diverse inbred strains of mice-NOD/LtJ, A/J, 129S1/SvImJ, FVB/NJ, C57BL/6J, WSB/EiJ, PWK/PhJ, and CAST/EiJ-to quantify the effects of genetic variation on the synaptic proteome between strains. Using iTRAQ-based quantitative proteome analyses, we detected significant differences in ∼20% of 400 core synaptic proteins. Surprisingly, the differentially abundant proteins showed a modest range of variation across strains, averaging about 1.3-fold. Analysis of protein abundance covariation across the eight strains identified known protein-protein relations (proteins of Arp2/3 complex), as well as novel relations (e.g. Dlg family, Fscn1). Moreover, covariation of synaptic proteins was substantially tighter (∼fourfold more dense than chance level) than corresponding networks of synaptic transcripts (∼twofold more dense than chance). The tight stoichiometry and coherent synaptic protein covariation networks suggest more intense evolutionary selection at this level of molecular organization. In conclusion, genetic diversity in the mouse genome differentially affects the transcriptome and proteome, and only partially penetrates the synaptic proteome. Protein abundance correlation analyses in genetically divergent strains can complement protein-protein interaction network analyses, to provide insight into protein interactomes.

  7. Genetic diversity in the feline leukemia virus gag gene.

    PubMed

    Kawamura, Maki; Watanabe, Shinya; Odahara, Yuka; Nakagawa, So; Endo, Yasuyuki; Tsujimoto, Hajime; Nishigaki, Kazuo

    2015-06-02

    Feline leukemia virus (FeLV) belongs to the Gammaretrovirus genus and is horizontally transmitted among cats. FeLV is known to undergo recombination with endogenous retroviruses already present in the host during FeLV-subgroup A infection. Such recombinant FeLVs, designated FeLV-subgroup B or FeLV-subgroup D, can be generated by transduced endogenous retroviral env sequences encoding the viral envelope. These recombinant viruses have biologically distinct properties and may mediate different disease outcomes. The generation of such recombinant viruses resulted in structural diversity of the FeLV particle and genetic diversity of the virus itself. FeLV env diversity through mutation and recombination has been studied, while gag diversity and its possible effects are less well understood. In this study, we investigated recombination events in the gag genes of FeLVs isolated from naturally infected cats and reference isolates. Recombination and phylogenetic analyses indicated that the gag genes often contain endogenous FeLV sequences and were occasionally replaced by entire endogenous FeLV gag genes. Phylogenetic reconstructions of FeLV gag sequences allowed for classification into three distinct clusters, similar to those previously established for the env gene. Analysis of the recombination junctions in FeLV gag indicated that these variants have similar recombination patterns within the same genotypes, indicating that the recombinant viruses were horizontally transmitted among cats. It remains to be investigated whether the recombinant sequences affect the molecular mechanism of FeLV transmission. These findings extend our understanding of gammaretrovirus evolutionary patterns in the field.

  8. Genetic Diversity in Chinese melon (Cucumis melo L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Melon (Cucumis melo L.; 2n = 2x = 24) is a morphologically diverse outcrossing Cucurbitaceae species. Genetically mapped random amplified polymorphic DNA (RAPD) markers have been used broadly to define genetic relationships (GR) among melon botanical groups and commercial market classes. Such inform...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    USGS Publications Warehouse

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

    2012-01-01

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

  11. Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation.

    PubMed

    Xie, Yan; Fan, Jibiao; Zhu, Weixi; Amombo, Erick; Lou, Yanhong; Chen, Liang; Fu, Jinmin

    2016-01-01

    Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices.

  12. Effect of Heavy Metals Pollution on Soil Microbial Diversity and Bermudagrass Genetic Variation

    PubMed Central

    Xie, Yan; Fan, Jibiao; Zhu, Weixi; Amombo, Erick; Lou, Yanhong; Chen, Liang; Fu, Jinmin

    2016-01-01

    Heavy metal pollution is a serious global environmental problem as it adversely affects plant growth and genetic variation. It also alters the composition and activity of soil microbial communities. The objectives of this study were to determine the soil microbial diversity, bermudagrass genetic variation in Cd contaminated or uncontaminated soils from Hunan province of China, and to evaluate Cd-tolerance of bermudagrass at different soils. The Biolog method, hydroponic experiments and simple sequence repeat markers were used to assess the functional diversity of microorganisms, Cd-tolerance and the genetic diversity of bermudagrass, respectively. Four of the sampling sites were heavily contaminated with heavy metals. The total bioactivity, richness, and microbial diversity decreased with increasing concentration of heavy metal. The hydroponic experiment revealed that bermudagrass populations collected from polluted sites have evolved, encompassing the feature of a higher resistance to Cd toxicity. Higher genetic diversity was observed to be more in contaminated populations than in uncontaminated populations. Heavy metal pollution can result in adverse effects on plant growth, soil microbial diversity and activity, and apparently has a stronger impact on the genetic structure. The results of this study provide new insights and a background to produce a genetic description of populations in a species that is suitable for use in phytoremediation practices. PMID:27303431

  13. Non-random distribution of individual genetic diversity along an environmental gradient

    PubMed Central

    Porlier, Mélody; Bélisle, Marc; Garant, Dany

    2009-01-01

    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

  14. Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

    USGS Publications Warehouse

    Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

    2008-01-01

    Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

  15. Promiscuity, sexual selection, and genetic diversity: a reply to Spurgin.

    PubMed

    Lifjeld, Jan T; Gohli, Jostein; Johnsen, Arild

    2013-10-01

    We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al.2013). Spurgin (2013) questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory.

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

    PubMed

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

    2015-02-01

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

  17. Salinity tolerance and genetic diversity of the dinoflagellate Oxyrrhis marina

    NASA Astrophysics Data System (ADS)

    Zhang, Jingyu; Li, Yun; Chen, Jiaxin

    2010-03-01

    To evaluate the relationship between salinity tolerance and genetic diversity of plankton, we collected a wild species of plankton from Taipingjiao, Qingdao. The fragment of ITS1-5.8S rDNA-ITS2 was extracted and sequenced. The results showed that the plankton belongs to Oxyrrhis marina. The salinity tolerance of O. marina ranges from 4 to 60. Seven selected groups were built up to evaluate salinity tolerance and to assess genetic diversity by RAPD. The salinity tolerance comparison revealed considerable differences among groups: the strains of O. marina in group 4 could survive under salinity from 4 to 32, while the strains selected for salinity 60 died under the salinity lower than 16. Analysis of genetic diversity of the seven groups showed that the mean genetic diversity index value was 0.28, but it was only 0.16 in selected group of 4 and was 0.24 for group 60. The result of AMOVA suggested a significantly positive relationship between the salinity tolerance and genetic diversity of O. marina ( P<0.01). This study indicates that consideration of intraspecific genetic divergence in O. marina might be indispensable when using it as a model in the study of salinity tolerance of wild plankton.

  18. High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

    PubMed

    Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

    2015-09-01

    Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.

  19. Genetic and Metabolite Diversity of Sardinian Populations of Helichrysum italicum

    PubMed Central

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

    2013-01-01

    Background Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. Methods H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. Key results The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. Conclusions The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil. PMID:24260149

  20. Rates of inbreeding and genetic diversity in Iranian Holstein cattle.

    PubMed

    Dadar, Mohsen; Mahyari, Saeid Ansari; Rokouei, Mohammad; Edriss, Mohammd Ali

    2014-10-01

    The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1,048,572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non-founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non-founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co-ancestry and inbreeding, which would lead to better handling of the effective population size.

  1. The structural diversity of artificial genetic polymers

    PubMed Central

    Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

    2016-01-01

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson–Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

  2. Unlocking the genetic diversity of Creole wheats.

    PubMed

    Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

    2016-03-15

    Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

  3. Unlocking the genetic diversity of Creole wheats

    PubMed Central

    Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

    2016-01-01

    Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement. PMID:26976656

  4. Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

    PubMed Central

    Rodriguez-Bonilla, Lorraine; Cuevas, Hugo E.; Montero-Rojas, Milly; Bird-Pico, Fernando; Luciano-Rosario, Dianiris; Siritunga, Dimuth

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388

  5. Genetic Diversity and Genome Complexity of Sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as a C4 plant, is one of the most efficient crops in converting solar energy into chemical energy. Sugarcane cultivar improvement programs have not yet systematically utilized the most of the genetic sources of yield potential and resistance to stresses that may exist in t...

  6. Genetic Diversity of US Sheep Breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic relationships between US sheep breeds is useful in developing conservation strategies and actions. A broad sampling of individual sheep from 28 breeds was performed. Breed types included: fine wool, meat types, long wool, hair, prolific, and fat tailed. Blood and semen samp...

  7. Ensuring the genetic diversity of potatoes

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies.

    PubMed

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  9. Stable genetic diversity despite parasite and pathogen spread in honey bee colonies

    NASA Astrophysics Data System (ADS)

    Jara, Laura; Muñoz, Irene; Cepero, Almudena; Martín-Hernández, Raquel; Serrano, José; Higes, Mariano; De la Rúa, Pilar

    2015-10-01

    In the last decades, the rapid spread of diseases, such as varroosis and nosemosis, associated with massive honey bee colonies mortality around the world has significantly decreased the number and size of honey bee populations and possibly their genetic diversity. Here, we compare the genetic diversity of Iberian honey bee colonies in two samplings performed in 2006 and 2010 in relation to the presence of the pathogenic agents Nosema apis, Nosema ceranae, and Varroa destructor in order to determine whether parasite and pathogen spread in honey bee colonies reflects changes in genetic diversity. We found that the genetic diversity remained similar, while the incidence of N. ceranae increased and the incidence of N. apis and V. destructor decreased slightly. These results indicate that the genetic diversity was not affected by the presence of these pathogenic agents in the analyzed period. However, the two groups of colonies with and without Nosema/Varroa detected showed significant genetic differentiation (G test). A detailed analysis of the allelic segregation of microsatellite loci in Nosema/Varroa-negative colonies and parasitized ones revealed two outlier loci related to genes involved in immune response.

  10. Impacts of genetic bottlenecks on soybean genome diversity

    PubMed Central

    Hyten, David L.; Song, Qijian; Zhu, Youlin; Choi, Ik-Young; Nelson, Randall L.; Costa, Jose M.; Specht, James E.; Shoemaker, Randy C.; Cregan, Perry B.

    2006-01-01

    Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare sequence variants and has undergone numerous allele frequency changes throughout its history. Although soybean genetic diversity has been eroded by human selection after domestication, it is notable that modern cultivars have retained 72% of the sequence diversity present in the Asian landraces but lost 79% of rare alleles (frequency ≤0.10) found in the Asian landraces. Simulations indicated that the diversity lost through the genetic bottlenecks of introduction and plant breeding was mostly due to the small number of Asian introductions and not the artificial selection subsequently imposed by selective breeding. The bottleneck with the most impact was domestication; when the low sequence diversity present in the wild species was halved, 81% of the rare alleles were lost, and 60% of the genes exhibited evidence of significant allele frequency changes. PMID:17068128

  11. Polishing the craft of genetic diversity creation in directed evolution.

    PubMed

    Tee, Kang Lan; Wong, Tuck Seng

    2013-12-01

    Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.

  12. Clonal structure and genetic diversity of three desert phreatophytes.

    PubMed

    Vonlanthen, Beatrix; Zhang, Ximing; Bruelheide, Helge

    2010-02-01

    The objective of this paper was to assess clone sizes of three perennial desert plant species with AFLP markers and to relate them to clonal and genetic diversity and to hydroecology. The study was carried out at the southern rim of the Taklamakan Desert, where sexual regeneration is only possible shortly after rare flooding events, resulting in rarely established cohorts with subsequent extensive vertical growth and horizontal clonal spread. In this environment, repeated seedling establishment is excluded. We expected decreasing clonal and genetic diversity with increasing clone size and increasing distance to the groundwater table and a common response pattern among all study species. Maximum sizes of Populus euphratica and Alhagi sparsifolia clones were 121 ha and 6.1 ha, respectively, while Tamarix ramosissima clones reached a maximum size of only 38 m(2). In P. euphratica and A. sparsifolia, clonal diversity declined with increasing clone size and increasing distance to the groundwater table, while genetic diversity remained unaffected. Tamarix ramosissima differed from the other species because of a much smaller clonality. Clone size and clonal diversity were found to be good proxy variables for clone age. Despite the considerable age of the clones, genetic diversity is maintained in the populations.

  13. Genotyping by sequencing reveals the genetic diversity of the USDA pisum diversity collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA expanded Pisum Single Plant (PSP) core collection is a unique resource that represents the breadth of the genetic diversity of the genus in an inbred format that facilitates genetic study. The collection includes inbred accessions from the refined pea core collection, parent lines of USDA r...

  14. Effect of fluoride pollution on genetic diversity of a medicinal tree, Syzygium cumini.

    PubMed

    Khan, Suphiya; Baunthiyal, Mamta; Kumari, Alka; Sharma, Vinay

    2012-07-01

    Syzygium cumini Linn. (Myrtaceae) is a medicinal tree (Jamun) used worldwide in treatment of diabetes. However, no molecular data is available on genetic polymorphism and its relationship, if any with fluoride pollution. In the present study, the genetic variability of two populations of S. cumini growing in fluoride rich soils and normal soils located in Rajasthan and Haryana regions of India, respectively was determined using random amplified polymorphic DNA (RAPD) markers. Different measures of diversity in Rajasthan populations: Shannon's index of phenotypic diversity (I) = 0.440; Nei's genetic diversity (h) = 0.292; effective number of alleles per locus (Ne) = 1.497; total species diversity (Hsp) = 0.307 and within population diversity (Hpop) = 0.158 showed high diversity in comparison to Haryana populations. Thus, it seems that Rajasthan population responds with increased genetic variation resulting possibly from new mutation that affect allele frequencies as a consequence of adaptation to contaminated environment. This may imply that the increased diversity levels may act as a buffer to combat fluoride stress. Cluster analysis and principal component analysis (PCA) results showed mixing between the populations.

  15. Speciation and genetic diversity in Centaurea subsect. Phalolepis in Anatolia

    PubMed Central

    López-Pujol, Jordi; López-Vinyallonga, Sara; Susanna, Alfonso; Ertuğrul, Kuddisi; Uysal, Tuna; Tugay, Osman; Guetat, Arbi; Garcia-Jacas, Núria

    2016-01-01

    Mountains of Anatolia are one of the main Mediterranean biodiversity hotspots and their richness in endemic species amounts for 30% of the flora. Two main factors may account for this high diversity: the complex orography and its role as refugia during past glaciations. We have investigated seven narrow endemics of Centaurea subsection Phalolepis from Anatolia by means of microsatellites and ecological niche modelling (ENM), in order to analyse genetic polymorphisms and getting insights into their speciation. Despite being narrow endemics, all the studied species show moderate to high SSR genetic diversity. Populations are genetically isolated, but exchange of genes probably occurred at glacial maxima (likely through the Anatolian mountain arches as suggested by the ENM). The lack of correlation between genetic clusters and (morpho) species is interpreted as a result of allopatric diversification on the basis of a shared gene pool. As suggested in a former study in Greece, post-glacial isolation in mountains would be the main driver of diversification in these plants; mountains of Anatolia would have acted as plant refugia, allowing the maintenance of high genetic diversity. Ancient gene flow between taxa that became sympatric during glaciations may also have contributed to the high levels of genetic diversity. PMID:27886271

  16. Creating polyketide diversity through genetic engineering.

    PubMed

    Kealey, James T

    2003-01-01

    Modular polyketide synthases (PKS) are large multifunctional enzymes that synthesize complex polyketides, a therapeutically important class of natural products. The linear order and composition of catalytic sites that comprise the PKS represent a "code" that determines the identity of the polyketide product. By re-programming the PKS through genetic engineering, it is possible to alter the code in a predictable manner to create specific structural modifications of polyketides and to produce new libraries of these natural products.

  17. Multiple paternities increase genetic diversity of offspring in Brandt's voles.

    PubMed

    Huo, Ying-jun; Wan, Xin-rong; Wolff, Jerry O; Wang, Guiming; Thomas, Shawn; Iglay, Raymond B; Leopold, Bruce D; Liu, Wei

    2010-07-01

    Mating system and philopatry influence the genetic structure of a social group in mammals. Brandt's vole (Lasiopodomys brandtii) lives in social groups year-round and has male biased dispersal, which makes the vole a model system for studies of genetic consequences of mating system and philopatry. This study aimed to test the hypotheses that: (1) multiple paternity (MP) would exist in Brandt's voles, enhance offspring genetic diversity and reduce genetic relatedness between littermates; (2) promiscuity would occur in this species in that males and females mate with multiple partners; and (3) plural breeders of a social group would be genetically related because of philopatry of female juveniles in Brandt's voles. Paternity analysis indicated that MP occurred in 11 (46%) of 24 social groups examined and that promiscuity existed in this species. Multiple paternity litters had twice the offspring genetic diversity and half the average within-litter genetic relatedness of single paternity litters. We also found plural breeding females in six social groups. Average pairwise genetic relatedness of plural breeders ranged from 0.41 to 0.72 in four social groups, suggesting first-order kinship. Future studies need to investigate effects of reproductive skew and MP on population genetic structure of Brandt's voles.

  18. [Genetic diversity of microbial communities in tea orchard soil].

    PubMed

    Xue, Dong; Yao, Huai-Ying; Huang, Chang-Yong

    2007-04-01

    In this paper, the total microbial DNA was extracted from the soils in 8-, 50- and 90 years old tea orchards, adjacent wasteland, and 90 years old forestland in Meijiawu tea area of Hangzhou. The 16S rDNA V3 fragment was amplified by PCR, and the polymorphism of this fragment was analyzed by DGGE. The results indicated that both the tea orchard age and the land use type had significant effects on soil microbial genetic diversity. There was a significant difference (P < 0.05) in the microbial genetic diversity index among wasteland, tea orchards and forestland, which was decreased in the order of wasteland > tea orchard > forestland. For the tea orchards of different ages, the soil microbial genetic diversity index, microbial biomass C, and basal respiration were significantly higher in 50 years old than in 8 and 90 years old tea orchards.

  19. The study of relatedness and genetic diversity in cranes

    USGS Publications Warehouse

    Gee, G.F.; Dessauer, H.C.; Longmire, J.; Briles, W.E.; Simon, R.C.; Wood, Don A.

    1992-01-01

    The U.S. Fish and Wildlife Service (Service) is responsible for recovery of endangered species in the wild and, when necessary, maintenance in captivity. These programs provide an immediate measure of insurance against extinction. A prerequisite inherent in all of these programs is the preservation of enough genetic diversity to maintain a viable population and to maintain the capacity of the population to respond to change. Measures of genetic diversity examine polymorphic genes that are not influenced by selection pressures. Examples of these techniques and those used to determine relatedness are discussed. Studies of genetic diversity, electrophoresis of blood proteins, relatedness, blood typing, and restriction fragment length polymorphisms which are being used by the Patuxent Wildlife Research Center are discussed in detail.

  20. Innate and adaptive immune traits are differentially affected by genetic and environmental factors

    PubMed Central

    Mangino, Massimo; Roederer, Mario; Beddall, Margaret H.; Nestle, Frank O.; Spector, Tim D.

    2017-01-01

    The diversity and activity of leukocytes is controlled by genetic and environmental influences to maintain balanced immune responses. However, the relative contribution of environmental compared with genetic factors that affect variations in immune traits is unknown. Here we analyse 23,394 immune phenotypes in 497 adult female twins. 76% of these traits show a predominantly heritable influence, whereas 24% are mostly influenced by environment. These data highlight the importance of shared childhood environmental influences such as diet, infections or microbes in shaping immune homeostasis for monocytes, B1 cells, γδ T cells and NKT cells, whereas dendritic cells, B2 cells, CD4+ T and CD8+ T cells are more influenced by genetics. Although leukocyte subsets are influenced by genetics and environment, adaptive immune traits are more affected by genetics, whereas innate immune traits are more affected by environment. PMID:28054551

  1. The stabilizing effects of genetic diversity on predator-prey dynamics.

    PubMed

    Steiner, Christopher F; Masse, Jordan

    2013-01-01

    Heterogeneity among prey in their susceptibility to predation is a potentially important stabilizer of predator-prey interactions, reducing the magnitude of population oscillations and enhancing total prey population abundance. When microevolutionary responses of prey populations occur at time scales comparable to population dynamics, adaptive responses in prey defense can, in theory, stabilize predator-prey dynamics and reduce top-down effects on prey abundance. While experiments have tested these predictions, less explored are the consequences of the evolution of prey phenotypes that can persist in both vulnerable and invulnerable classes. We tested this experimentally using a laboratory aquatic system composed of the rotifer Brachionus calyciflorus as a predator and the prey Synura petersenii, a colony-forming alga that exhibits genetic variation in its propensity to form colonies and colony size (larger colonies are a defense against predators). Prey populations of either low initial genetic diversity and low adaptive capacity or high initial genetic diversity and high adaptive capacity were crossed with predator presence and absence. Dynamics measured over the last 127 days of the 167-day experiment revealed no effects of initial prey genetic diversity on the average abundance or temporal variability of predator populations. However, genetic diversity and predator presence/absence interactively affected prey population abundance and stability; diversity of prey had no effects in the absence of predators but stabilized dynamics and increased total prey abundance in the presence of predators. The size structure of the genetically diverse prey populations diverged from single strain populations in the presence of predators, showing increases in colony size and in the relative abundance of cells found in colonies. Our work sheds light on the adaptive value of colony formation and supports the general view that genetic diversity and intraspecific trait variation of

  2. Mapping Viral Functional Domains for Genetic Diversity in Plants

    PubMed Central

    Pita, Justin S.

    2013-01-01

    Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3′ nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism. PMID:23115283

  3. Invasive Predators Deplete Genetic Diversity of Island Lizards

    PubMed Central

    Gasc, Amandine; Duryea, M. C.; Cox, Robert M.; Kern, Andrew; Calsbeek, Ryan

    2010-01-01

    Invasive species can dramatically impact natural populations, especially those living on islands. Though numerous examples illustrate the ecological impact of invasive predators, no study has examined the genetic consequences for native populations subject to invasion. Here we capitalize on a natural experiment in which a long-term study of the brown anole lizard (Anolis sagrei) was interrupted by rat invasion. An island population that was devastated by rats recovered numerically following rat extermination. However, population genetic analyses at six microsatellite loci suggested a possible loss of genetic diversity due to invasion when compared to an uninvaded island studied over the same time frame. Our results provide partial support for the hypothesis that invasive predators can impact the genetic diversity of resident island populations. PMID:20706576

  4. Genetic and functional diversity of propagating cells in glioblastoma.

    PubMed

    Piccirillo, Sara G M; Colman, Sue; Potter, Nicola E; van Delft, Frederik W; Lillis, Suzanne; Carnicer, Maria-Jose; Kearney, Lyndal; Watts, Colin; Greaves, Mel

    2015-01-13

    Glioblastoma (GBM) is a lethal malignancy whose clinical intransigence has been linked to extensive intraclonal genetic and phenotypic diversity and the common emergence of therapeutic resistance. This interpretation embodies the implicit assumption that cancer stem cells or tumor-propagating cells are themselves genetically and functionally diverse. To test this, we screened primary GBM tumors by SNP array to identify copy number alterations (a minimum of three) that could be visualized in single cells by multicolor fluorescence in situ hybridization. Interrogation of neurosphere-derived cells (from four patients) and cells derived from secondary transplants of these same cells in NOD-SCID mice allowed us to infer the clonal and phylogenetic architectures. Whole-exome sequencing and single-cell genetic analysis in one case revealed a more complex clonal structure. This proof-of-principle experiment revealed that subclones in each GBM had variable regenerative or stem cell activity, and highlighted genetic alterations associated with more competitive propagating activity in vivo.

  5. [Application of ISSR technology in genetic diversity detection of jute].

    PubMed

    Qi, Jianmin; Zhou, Dongxin; Wu, Weiren; Lin, Lihui; Wu, Jianmei; Fang, Pingping

    2003-09-01

    The genetic diversity among 27 accessions of Corchorus, including 10 Jute species, was investigated with ISSR technique. 283 DNA bands were amplified with 25 ISSR primers, among which, 263 (92.85%) were polymorphic, with 10.48 bands per primer in average. A further systemic cluster analysis indicated that the accessions could be clustered into three groups, and the group II (including two cultispecies and their close wild species) was obviously genetically different from the groups I and III (including eight wild species). Moreover, 16 accessions in group II presented a higher intraspecific genetic resemblance, while 11 accessions among groups I & III showed an abundant interspecific genetic diversity. After synthesized the relevant findings of morphology and DNA classification, it's found that C. urticifolius could be one of the original wild species, C. tilaculariszic was a variation of C. tilaculari, and Tian Jute could be an untitled wild species.

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

    PubMed

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

    2015-12-07

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

  7. Assessment of genetic diversity in Brazilian barley using SSR markers

    PubMed Central

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  10. Genetic Diversity and Population Structure of Teosinte

    PubMed Central

    Fukunaga, Kenji; Hill, Jason; Vigouroux, Yves; Matsuoka, Yoshihiro; Sanchez G., Jesus; Liu, Kejun; Buckler, Edward S.; Doebley, John

    2005-01-01

    The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes. PMID:15687282

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

    PubMed

    Lv, Jing; Qi, Jianjian; Shi, Qiuxiang; Shen, Di; Zhang, Shengping; Shao, Guangjin; Li, Hang; Sun, Zhanyong; Weng, Yiqun; Shang, Yi; Gu, Xingfang; Li, Xixiang; Zhu, Xiaoguo; Zhang, Jinzhe; van Treuren, Robbert; van Dooijeweert, Willem; Zhang, Zhonghua; Huang, Sanwen

    2012-01-01

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

  12. Genome-wide genetic diversity of rove beetle populations along a metal pollution gradient.

    PubMed

    Giska, Iwona; Babik, Wiesław; van Gestel, Cornelis A M; van Straalen, Nico M; Laskowski, Ryszard

    2015-09-01

    To what extent chemical contamination affects genetic diversity of wild populations remains an open question in ecotoxicology. Here we used a genome-wide approach (615 nuclear RADseq loci containing 3017 SNPs) and a mtDNA fragment (ATP6) to analyze the effect of long-term exposure to elevated concentrations of metals (Cd, Pb, Zn) on genetic diversity in rove beetle (Staphylinus erythropterus) populations living along a pollution gradient in Poland. In total, 96 individuals collected from six sites at increasing distance from the source of pollution were analyzed. We found weak differentiation between populations suggesting extensive gene flow. The highest genetic diversity was observed in a population inhabiting the polluted site with the highest metal availability. This may suggest increased mutation rates, possibly in relation to elevated oxidative stress levels. The polluted site could also act as an ecological sink receiving numerous migrants from neighboring populations. Despite higher genetic diversity at the most polluted site, there was no correlation between the genetic diversity and metal pollution or other soil properties. We did not find a clear genomic signature of local adaptation to metal pollution. Like in some other cases of metal tolerance in soil invertebrates, high mobility may counteract possible effects of local selective forces associated with soil pollution.

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

    PubMed

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

    2016-03-01

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

  14. Positive correlation between genetic diversity and fitness in a large, well-connected metapopulation

    PubMed Central

    Vandewoestijne, Sofie; Schtickzelle, Nicolas; Baguette, Michel

    2008-01-01

    Background Theory predicts that lower dispersal, and associated gene flow, leads to decreased genetic diversity in small isolated populations, which generates adverse consequences for fitness, and subsequently for demography. Here we report for the first time this effect in a well-connected natural butterfly metapopulation with high population densities at the edge of its distribution range. Results We demonstrate that: (1) lower genetic diversity was coupled to a sharp decrease in adult lifetime expectancy, a key component of individual fitness; (2) genetic diversity was positively correlated to the number of dispersing individuals (indicative of landscape functional connectivity) and adult population size; (3) parameters inferred from capture-recapture procedures (population size and dispersal events between patches) correlated much better with genetic diversity than estimates usually used as surrogates for population size (patch area and descriptors of habitat quality) and dispersal (structural connectivity index). Conclusion Our results suggest that dispersal is a very important factor maintaining genetic diversity. Even at a very local spatial scale in a metapopulation consisting of large high-density populations interconnected by considerable dispersal rates, genetic diversity can be decreased and directly affect the fitness of individuals. From a biodiversity conservation perspective, this study clearly shows the benefits of both in-depth demographic and genetic analyses. Accordingly, to ensure the long-term survival of populations, conservation actions should not be blindly based on patch area and structural isolation. This result may be especially pertinent for species at their range margins, particularly in this era of rapid environmental change. PMID:18986515

  15. Parasites and genetic diversity in an invasive bumblebee

    PubMed Central

    Jones, Catherine M; Brown, Mark J F; Ings, Thomas

    2014-01-01

    Biological invasions are facilitated by the global transportation of species and climate change. Given that invasions may cause ecological and economic damage and pose a major threat to biodiversity, understanding the mechanisms behind invasion success is essential. Both the release of non-native populations from natural enemies, such as parasites, and the genetic diversity of these populations may play key roles in their invasion success. We investigated the roles of parasite communities, through enemy release and parasite acquisition, and genetic diversity in the invasion success of the non-native bumblebee, Bombus hypnorum, in the United Kingdom. The invasive B. hypnorum had higher parasite prevalence than most, or all native congeners for two high-impact parasites, probably due to higher susceptibility and parasite acquisition. Consequently parasites had a higher impact on B. hypnorum queens’ survival and colony-founding success than on native species. Bombus hypnorum also had lower functional genetic diversity at the sex-determining locus than native species. Higher parasite prevalence and lower genetic diversity have not prevented the rapid invasion of the United Kingdom by B. hypnorum. These data may inform our understanding of similar invasions by commercial bumblebees around the world. This study suggests that concerns about parasite impacts on the small founding populations common to re-introduction and translocation programs may be less important than currently believed. PMID:24749545

  16. Worldwide genetic diversity for mineral element concentrations in rice grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the aim of identifying rice (Oryza spp.) germplasm having enhanced grain nutritional value, the mineral nutrient and trace element content (a.k.a. ionome) of whole (unmilled) grains from a set of 1763 rice accessions of diverse geographic and genetic origin were evaluated. Seed for analysis o...

  17. Coalescence and genetic diversity in sexual populations under selection.

    PubMed

    Neher, Richard A; Kessinger, Taylor A; Shraiman, Boris I

    2013-09-24

    In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic "linkage block" with a characteristic length, , determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra compared with computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. Assessing genetic diversity in Valencia peanut germplasm using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Valencia peanuts (Arachis hypogaea L.ssp. fastigiata var. fastigiata) are well known for their in-shell market value. Assessment of genetic diversity of the available Valencia germplasm is key to the success of developing improved cultivars with desirable agronomic and quality traits. In the pres...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. Genomovars and genomes: Deciphering the genetic diversity of Flavobacterium columnare

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Columnaris disease, caused by the Gram-negative bacterium Flavobacterium columnare, is one of the leading causes of disease losses to the catfish industry in the Southeast USA. An exceptionally high level of genetic diversity among isolates of F. columnare has long been recognized, yet very little h...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. Analysis of mitochondrial genetic diversity of Ustilago maydis in Mexico.

    PubMed

    Jiménez-Becerril, María F; Hernández-Delgado, Sanjuana; Solís-Oba, Myrna; González Prieto, Juan M

    2016-10-11

    The current understanding of the genetic diversity of the phytopathogenic fungus Ustilago maydis is limited. To determine the genetic diversity and structure of U. maydis, 48 fungal isolates were analyzed using mitochondrial simple sequence repeats (SSRs). Tumours (corn smut or 'huitlacoche') were collected from different Mexican states with diverse environmental conditions. Using bioinformatic tools, five microsatellites were identified within intergenic regions of the U. maydis mitochondrial genome. SSRMUM4 was the most polymorphic marker. The most common repeats were hexanucleotides. A total of 12 allelic variants were identified, with a mean of 2.4 alleles per locus. An estimate of the genetic diversity using analysis of molecular variance (AMOVA) revealed that the highest variance component is within states (84%), with moderate genetic differentiation between states (16%) (FST = 0.158). A dendrogram generated using the unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure grouped the U. maydis isolates into two subgroups (K = 2) based on their shared SSRs.

  4. Estimation of genetic diversity using SSR markers in sunflower

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sunflower is a major oilseed crop in central Asia, but little is known of the molecular diversity among collections of sunflower from Pakistan region. This paper described inherent genetic relationships among sunflower collections using Simple Sequence Repeat molecular markers. Results should help...

  5. High genetic differentiation and cross-shelf patterns of genetic diversity among Great Barrier Reef populations of Symbiodinium

    NASA Astrophysics Data System (ADS)

    Howells, E. J.; van Oppen, M. J. H.; Willis, B. L.

    2009-03-01

    The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales from 16 to 1,360 km (pairwise ΦST = 0.01-0.47, mean = 0.22); the only exception being two neighbouring populations in the Cairns region separated by 17 km. This indicates that gene flow is restricted for Symbiodinium C hosted by S. flexibilis on the GBR. Patterns of population structure reflect longshore circulation patterns and limited cross-shelf mixing, suggesting that passive transport by currents is the primary mechanism of dispersal in Symbiodinium types that are acquired horizontally. There was no correlation between the genetic structure of Symbiodinium populations and their host S. flexibilis, most likely because different factors affect the dispersal and recruitment of each partner in the symbiosis. The genetic diversity of these Symbiodinium reef populations is on average 1.5 times lower on inshore reefs than on offshore reefs. Lower inshore diversity may reflect the impact of recent bleaching events on Sinularia assemblages, which have been more widespread and severe on inshore reefs, but may also have been shaped by historical sea level fluctuations or recent migration patterns.

  6. Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

    PubMed Central

    Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

    2014-01-01

    Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation. PMID:25333788

  7. Genetic diversity and structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China.

    PubMed

    Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

    2014-01-01

    Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation.

  8. Review of genetic diversity in malaria vectors (Culicidae: Anophelinae).

    PubMed

    Loaiza, J R; Bermingham, E; Sanjur, O I; Scott, M E; Bickersmith, S A; Conn, J E

    2012-01-01

    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 facilitated the evaluation of the contribution of historical demographic processes to genetic structure. A common pattern of past unstable demography (i.e., historical fluctuation in the effective population size) by several Anopheles species, regardless of methodology (DNA markers), mosquito ecology (anthropophilic vs zoophilic), vector status (primary vs secondary) and geographical distribution, suggests that Pleistocene environmental changes were major drivers of divergence at population and species levels worldwide.

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

    PubMed

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

    2010-09-01

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

  10. [Screening of peafowl microsatellite primers and analysis of genetic diversity].

    PubMed

    Bao, Wen-Bin; Chen, Guo-Hong; Shu, Jing-Ting; Xu, Qi; Li, Hui-Fang

    2006-10-01

    The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing.

  11. Synthetic biology: advancing the design of diverse genetic systems

    PubMed Central

    Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

    2013-01-01

    A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

  12. Genetic and phenotypic diversity in breast tumor metastases

    PubMed Central

    Almendro, Vanessa; Kim, Hee Jung; Cheng, Yu-Kang; Gönen, Mithat; Itzkovitz, Shalev; Argani, Pedram; van Oudenaarden, Alexander; Sukumar, Saraswati; Michor, Franziska; Polyak, Kornelia

    2014-01-01

    Metastatic disease is the main cause of cancer-related mortality due to almost universal therapeutic resistance. Despite its high clinical relevance our knowledge of how cancer cell populations change during metastatic progression is limited. Here we investigated intratumor genetic and phenotypic heterogeneity during metastatic progression of breast cancer. We analyzed cellular genotypes and phenotypes at the single cell level by performing immuno-FISH in intact tissue sections of distant metastatic tumors from rapid autopsy cases and from primary tumors and matched lymph node metastases collected prior to systemic therapy. We calculated Shannon index of intratumor diversity in all cancer cells and within phneotypically distinct cell populations. We found that the extent of intratumor genetic diversity was similar regardless of the chromosomal region analyzed, implying that it may reflect an inherent property of the tumors. We observed that genetic diversity was highest in distant metastases and was generally concordant across lesions within the same patient, whereas treatment-naïve primary tumors and matched lymph node metastases were frequently genetically more divergent. In contrast, cellular phenotypes were more discordant between distant metastases than primary tumors and matched lymph node metastases. Diversity for 8q24 was consistently higher in HER2+ tumors compared to other subtypes and in metastases of triple negative tumors relative to primary sites. We conclude that our integrative method that couples ecologic models with experimental data in human tissue samples, could be used for the improved prognostication of cancer patients and for the design of more effective therapies for progressive disease. Major findings By defining quantitative measures of intratumor cellular genetic and phenotypic heterogeneity in primary and metastatic breast tumors and by assessing tumor topology, we determined that distant metastatic tumors are the most diverse, which

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

    PubMed Central

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G”ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands. PMID:26079603

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

    PubMed

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

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

  15. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

    PubMed Central

    Martin, Simon H.; Möst, Markus; Palmer, William J.; Salazar, Camilo; McMillan, W. Owen; Jiggins, Francis M.; Jiggins, Chris D.

    2016-01-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. PMID:27017626

  16. African diversity may hold key to human origins, medical questions. Genetic diversity.

    PubMed

    1999-02-01

    The genetic diversity of human populations in Africa has been studied less in Africa than it has been in Europe and Asia. However, the study of such diversity in Africa is important to the determination of where, when, and how modern humans evolved; to gain insight into the genetic diseases of Africans and African-Americans; and to identify potential treatments for diseases like malaria and HIV. Dr. Sarah Tishkoff et al.'s study of 3 locations on DNA samples from 13-18 populations in Africa and 30-45 other populations in other parts of the world found extremely high genetic diversity both within and between the African populations, and much less diversity in non-African populations. Tishkoff's research team examined the genetic information inherited from both the father and mother, which exists upon a strand of DNA close enough together that the markers are transferred intact. The use of genetic markers to trace lineages found that modern humans appear to have emerged from Africa 100,000-150,000 years ago and that the population which left Africa was rather small. These data agree with earlier research findings. The findings of Tishkoff et al. also suggest that the group which migrated from Africa came from northern East Africa.

  17. Functional roles affect diversity-succession relationships for boreal beetles.

    PubMed

    Gibb, Heloise; Johansson, Therese; Stenbacka, Fredrik; Hjältén, Joakim

    2013-01-01

    Species diversity commonly increases with succession and this relationship is an important justification for conserving large areas of old-growth habitats. However, species with different ecological roles respond differently to succession. We examined the relationship between a range of diversity measures and time since disturbance for boreal forest beetles collected over a 285 year forest chronosequence. We compared responses of "functional" groups related to threat status, dependence on dead wood habitats, diet and the type of trap in which they were collected (indicative of the breadth of ecologies of species). We examined fits of commonly used rank-abundance models for each age class and traditional and derived diversity indices. Rank abundance distributions were closest to the Zipf-Mandelbrot distribution, suggesting little role for competition in structuring most assemblages. Diversity measures for most functional groups increased with succession, but differences in slopes were common. Evenness declined with succession; more so for red-listed species than common species. Saproxylic species increased in diversity with succession while non-saproxylic species did not. Slopes for fungivores were steeper than other diet groups, while detritivores were not strongly affected by succession. Species trapped using emergence traps (log specialists) responded more weakly to succession than those trapped using flight intercept traps (representing a broader set of ecologies). Species associated with microhabitats that accumulate with succession (fungi and dead wood) thus showed the strongest diversity responses to succession. These clear differences between functional group responses to forest succession should be considered in planning landscapes for optimum conservation value, particularly functional resilience.

  18. Functional Roles Affect Diversity-Succession Relationships for Boreal Beetles

    PubMed Central

    Gibb, Heloise; Johansson, Therese; Stenbacka, Fredrik; Hjältén, Joakim

    2013-01-01

    Species diversity commonly increases with succession and this relationship is an important justification for conserving large areas of old-growth habitats. However, species with different ecological roles respond differently to succession. We examined the relationship between a range of diversity measures and time since disturbance for boreal forest beetles collected over a 285 year forest chronosequence. We compared responses of “functional” groups related to threat status, dependence on dead wood habitats, diet and the type of trap in which they were collected (indicative of the breadth of ecologies of species). We examined fits of commonly used rank-abundance models for each age class and traditional and derived diversity indices. Rank abundance distributions were closest to the Zipf-Mandelbrot distribution, suggesting little role for competition in structuring most assemblages. Diversity measures for most functional groups increased with succession, but differences in slopes were common. Evenness declined with succession; more so for red-listed species than common species. Saproxylic species increased in diversity with succession while non-saproxylic species did not. Slopes for fungivores were steeper than other diet groups, while detritivores were not strongly affected by succession. Species trapped using emergence traps (log specialists) responded more weakly to succession than those trapped using flight intercept traps (representing a broader set of ecologies). Species associated with microhabitats that accumulate with succession (fungi and dead wood) thus showed the strongest diversity responses to succession. These clear differences between functional group responses to forest succession should be considered in planning landscapes for optimum conservation value, particularly functional resilience. PMID:23977350

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. Rapid anti-pathogen response in ant societies relies on high genetic diversity

    PubMed Central

    Ugelvig, Line V.; Kronauer, Daniel J. C.; Schrempf, Alexandra; Heinze, Jürgen; Cremer, Sylvia

    2010-01-01

    Social organisms are constantly exposed to infectious agents via physical contact with conspecifics. While previous work has shown that disease susceptibility at the individual and group level is influenced by genetic diversity within and between group members, it remains poorly understood how group-level resistance to pathogens relates directly to individual physiology, defence behaviour and social interactions. We investigated the effects of high versus low genetic diversity on both the individual and collective disease defences in the ant Cardiocondyla obscurior. We compared the antiseptic behaviours (grooming and hygienic behaviour) of workers from genetically homogeneous and diverse colonies after exposure of their brood to the entomopathogenic fungus Metarhizium anisopliae. While workers from diverse colonies performed intensive allogrooming and quickly removed larvae covered with live fungal spores from the nest, workers from homogeneous colonies only removed sick larvae late after infection. This difference was not caused by a reduced repertoire of antiseptic behaviours or a generally decreased brood care activity in ants from homogeneous colonies. Our data instead suggest that reduced genetic diversity compromises the ability of Cardiocondyla colonies to quickly detect or react to the presence of pathogenic fungal spores before an infection is established, thereby affecting the dynamics of social immunity in the colony. PMID:20444720

  1. Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation.

    PubMed

    Hoffman, J I; Dasmahapatra, K K; Amos, W; Phillips, C D; Gelatt, T S; Bickham, J W

    2009-07-01

    Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA (mtDNA) and microsatellite data sets, we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity were found at the three markers, with Nei's gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.

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

    PubMed

    de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

    2013-03-01

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

  3. Migration distance rather than migration rate explains genetic diversity in human patrilocal groups.

    PubMed

    Marks, Sarah J; Levy, Hila; Martinez-Cadenas, Conrado; Montinaro, Francesco; Capelli, Cristian

    2012-10-01

    In patrilocal groups, females preferentially move to join their mate's paternal relatives. The gender-biased gene flow generated by this cultural practice is expected to affect genetic diversity across human populations. Greater female than male migration is predicted to result in a larger decrease in between-group differentiation for mitochondrial DNA (mtDNA) than for the non-recombining part of the Y chromosome (NRY). We address the question of how patrilocality affects the distribution of genetic variation in human populations controlling for confounding factors such as ethno-linguistic heterogeneity and geographic distance which possibly explain the contradictory results observed in previous studies. By combining genetic and bio-demographic data from Lesotho and Spain, we show that preferential female migration over short distances appears to minimize the impact of a generally higher female migration rate in patrilocal communities, suggesting patrilocality might influence genetic variation only at short ranges.

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

    PubMed

    Moura, E F; de Oliveira, M S P

    2012-11-26

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

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

    PubMed

    Gell, Gyöngyvér; Balázs, Ervin; Petrik, Kathrin

    2010-04-01

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

  6. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity

    PubMed Central

    Rafat, Arash; Ridden, Johnathon D.; Cruickshank, Robert H.; Ridgway, Hayley J.; Paterson, Adrian M.

    2014-01-01

    The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in their phylogenetic

  7. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

    PubMed

    Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

    2014-01-01

    The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence

  8. The 'Out of Africa' Hypothesis, Human Genetic Diversity, and Comparative Economic Development

    PubMed Central

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

    This research argues that deep-rooted factors, determined tens of thousands of years ago, had a significant effect on the course of economic development from the dawn of human civilization to the contemporary era. It advances and empirically establishes the hypothesis that, in the course of the exodus of Homo sapiens out of Africa, variation in migratory distance from the cradle of humankind to various settlements across the globe affected genetic diversity and has had a long-lasting effect on the pattern of comparative economic development that is not captured by geographical, institutional, and cultural factors. In particular, the level of genetic diversity within a society is found to have a hump-shaped effect on development outcomes in both the pre-colonial and the modern era, reflecting the trade-off between the beneficial and the detrimental effects of diversity on productivity. While the intermediate level of genetic diversity prevalent among Asian and European populations has been conducive for development, the high degree of diversity among African populations and the low degree of diversity among Native American populations have been a detrimental force in the development of these regions. PMID:25506083

  9. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth.

  10. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies.

    PubMed

    Nyman, Tommi; Valtonen, Mia; Aspi, Jouni; Ruokonen, Minna; Kunnasranta, Mervi; Palo, Jukka U

    2014-09-01

    Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea 'mainland' and two the 'aquatic islands' composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.

  11. Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

    PubMed Central

    Nyman, Tommi; Valtonen, Mia; Aspi, Jouni; Ruokonen, Minna; Kunnasranta, Mervi; Palo, Jukka U

    2014-01-01

    Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea ‘mainland’ and two the ‘aquatic islands’ composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea. PMID:25535558

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

    PubMed Central

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

    2015-01-01

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

  13. Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary.

    PubMed

    Ács, Zoltán; Hayward, Alexander; Sugár, László

    2016-09-01

    Dictyocaulus nematode worms live as parasites in the lower airways of ungulates and can cause significant disease in both wild and farmed hosts. This study represents the first population genetic analysis of large lungworms in wildlife. Specifically, we quantify genetic variation in Dictyocaulus lungworms from wild deer (red deer, fallow deer and roe deer) in Hungary, based on mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data, using population genetic and phylogenetic analyses. The studied Dictyocaulus taxa display considerable genetic diversity. At least one cryptic species and a new parasite-host relationship are revealed by our molecular study. Population genetic analyses for Dictyocaulus eckerti revealed high gene flow amongst weakly structured spatial populations that utilise the three host deer species considered here. Our results suggest that D. eckerti is a widespread generalist parasite in ungulates, with a diverse genetic backround and high evolutionary potential. In contrast, evidence of cryptic genetic structure at regional geographic scales was observed for Dictyocaulus capreolus, which infects just one host species, suggesting it is a specialist within the studied area. D. capreolus displayed lower genetic diversity overall, with only moderate gene flow compared to the closely related D. eckerti. We suggest that the differing vagility and dispersal behaviour of hosts are important contributing factors to the population structure of lungworms, and possibly other nematode parasites with single-host life cycles. Our findings are of relevance for the management of lungworms in deer farms and wild deer populations.

  14. Mobile Introns Shape the Genetic Diversity of Their Host Genes

    PubMed Central

    Repar, Jelena; Warnecke, Tobias

    2017-01-01

    Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose nonrandom patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. Through multiple lines of evidence, we rule out relaxed purifying selection as the cause of uneven nucleotide diversity. Instead, our findings implicate intron mobility as a direct driver of host gene diversity. We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or nonrandom patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to empty target sites via homologous recombination. Importantly, however, we show that exonic coconversion can only explain diversity gradients near intron–exon boundaries if the conversion template comes from outside the population. In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations. PMID:28193728

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

    PubMed

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

    2013-08-01

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

  16. GENETIC DIVERSITY AND THE ORIGINS OF CULTURAL FRAGMENTATION

    PubMed Central

    Ashraf, Quamrul; Galor, Oded

    2013-01-01

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

  17. Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

    PubMed Central

    Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

  18. ASSOCIATIONS BETWEEN GENETIC DIVERSITY AND ANTHROPOGENIC DISTURBANCE IN MIDWESTERN STREAM-DWELLING MINNOWS

    EPA Science Inventory

    Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...

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

    PubMed

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

    2010-06-01

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

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

    PubMed

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

    2009-07-01

    In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.

  1. Molecular phylogeography and genetic diversity of East Asian goats.

    PubMed

    Lin, B Z; Odahara, S; Ishida, M; Kato, T; Sasazaki, S; Nozawa, K; Mannen, H

    2013-02-01

    The domestic goat is one of the most important livestock species, but its origins and genetic diversity still remain uncertain. Multiple highly divergent maternal lineages of goat have been reported in previous studies. Although one of the mitochondrial DNA lineages, lineage B, was detected only in eastern and southern Asia, the geographic distribution of these lineages was previously unclear. Here, we examine the genetic diversity and phylogeographic structure of Asian goats by mitochondrial DNA sequences and morphological characteristics. The analyses of a total of 1661 Asian goats from 12 countries revealed a high frequency of lineage B in Southeast Asia. The frequency of this lineage tended to be higher in mountain areas than in plain areas in Southeast Asian countries, and there was a significant correlation between its frequency and morphological traits. The results suggest an original predominance of lineage B in Southeast Asia and the recent infiltration of lineage A into Southeast Asian goats.

  2. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

    PubMed

    Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

    2016-05-01

    A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.

  3. Mitochondrial genetic diversity, phylogeny and population structure of Hydropotes inermis in South Korea.

    PubMed

    Kim, Baek-Jun; Lee, Yun-Sun; Park, Yong-Su; Kim, Kyung Seok; Min, Mi-Sook; Lee, Sang-Don; Lee, Hang

    2014-01-01

    The water deer (Hydropotes inermis) is one of the rarest species of deer in the family Cervidae. Only two subspecies exist in East Asia, and few studies have examined the genetic characteristics of the species. Here, we investigated the genetic diversity, phylogeny and population differentiation of the Korean subspecies (H. inermis argyropus). Seventeen mitochondrial D-loop haplotypes (822 bp) were detected and analyzed from 107 individual samples, together with a Chinese subspecies (H. inermis inermis) haplotype. The genetic diversity of the Korean subspecies is lower (π = 0.756%, h = 0.867) than that of the Chinese subspecies estimated in a previous study. This low genetic diversity may result from historical anthropogenic disturbances and/or a founder effect during the glacial period. The phylogenetic tree and median-joining network showed no location-specific distribution of D-loop haplotypes, but revealed two major lineages, A and B, of water deer. The A and B lineages were separated from each other at the beginning of the Pleistocene era (2.1-1.3 million years ago), with a genetic divergence of 1.332 ± 0.340%. The genetic divergence within lineages A and B was 0.525 ± 0.167% and 0.264 ± 0.113%, respectively. This suggests that climate change affected the division of the two lineages. Water deer sampled from the three Korean regions (26 locations) were slightly distinct in their genetic structure (AMOVA: F(ST) = 0.28416, P < 0.00001; Φ(ST) = 0.19239, P < 0.00001). Such slight population differentiation may be derived from differential dispersal ability in males and females. The use of genetic markers, such as nuclear microsatellite and Y-linked DNA markers, and samples collected from various localities in East Asia should improve our understanding of the water deer's genetic characteristics.

  4. Molecular diversity analysis of eggplant (Solanum melongena) genetic resources.

    PubMed

    Ali, Z; Xu, Z L; Zhang, D Y; He, X L; Bahadur, S; Yi, J X

    2011-06-14

    Eggplant (Solanum melongena), a vegetable that is cultivated worldwide, is of considerable importance to agriculture in China. We analyzed the diversity of this plant using inter-simple sequence repeat (ISSR) and RAPD procedures to subdivide 143 Chinese-cultivated eggplants based on coefficient of parentage, genetic diversity index (GDI) and canonical discriminant analysis. ISSR markers were more effective than RAPD markers for detecting genetic diversity, which ranged from 0.10-0.51, slightly lower than what is known from other crops. Our ISSR/RAPD data provide molecular evidence that coincides with morphological-based classification into three varieties and further subdivision into eight groups, except for two groups. Intensive use of elite parents and extensive crossing within groups have resulted in increased coefficient of parentage and proportional contribution but decreased GDI during the past decades. The mean coefficient of parentage and proportional contribution increased from 0.05 to 0.10% and from 3.22 to 6.46% during 1980-1991 and 1992-2003, respectively. The GDI of landraces was 0.21, higher than the 0.09 and 0.08 calculated for the hybrid cultivars released during the two periods. The recent introduction of alien genotypes into eggplant breeding programs may broaden the genetic base.

  5. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    PubMed

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  6. On the Consequences of Purging and Linkage on Fitness and Genetic Diversity

    PubMed Central

    Bersabé, Diego; Caballero, Armando; Pérez-Figueroa, Andrés; García-Dorado, Aurora

    2015-01-01

    Using computer simulation we explore the consequences of linkage on the inbreeding load of an equilibrium population, and on the efficiency of purging and the loss of genetic diversity after a reduction in population size. We find that linkage tends to cause increased inbreeding load due to the build up of coupling groups of (partially) recessive deleterious alleles. It also induces associative overdominance at neutral sites but rarely causes increased neutral genetic diversity in equilibrium populations. After a reduction in population size, linkage can cause some delay both for the expression of the inbreeding load and the corresponding purging. However, reasonable predictions can be obtained for the evolution of fitness under inbreeding and purging by using empirical estimates of the inbreeding depression rate. Purging selection against homozygotes for deleterious alleles affects the population’s pedigree. Furthermore, it can slow the loss of genetic diversity compared to that expected from the variance of gametic contributions to the breeding group and even from pedigree inbreeding. Under some conditions, this can lead to a smaller loss of genetic diversity, even below that expected from population size in the absence of selection. PMID:26564947

  7. Genetic diversity of hydrothermal-vent barnacles in Manus Basin

    NASA Astrophysics Data System (ADS)

    Plouviez, Sophie; Schultz, Thomas F.; McGinnis, Gwendolyn; Minshall, Halle; Rudder, Meghan; Van Dover, Cindy L.

    2013-12-01

    We evaluated mitochondrial cytochrome oxidase I genetic diversity of two barnacle species (Eochionelasmus ohtai manusensis, Vulcanolepas cf. parensis) at three sites in Manus Basin (Solwara 1, South Su, Solwara 8). There was no evidence for within-site or between-site genetic differentiation for either species. While E. ohtai manusensis showed limited genetic variation, V. cf. parensis showed greater variation, with sequences distributed between two divergent groups. Assuming the cytochrome oxidase I gene is not under selection, significantly negative Tajima's D in E. ohtai manusensis is consistent with a recent population expansion due to a bottleneck or founder effect, whereas V. cf. parensis (combined groups) did not depart from a stable effective population size. Considering the groups separately, V. cf. parensis Group 1 (but not Group 2) showed a negative Tajima's D, indicating these groups may have encountered different historical demographic conditions. Data reported here are part of a baseline study against which recovery of genetic diversity following mineral extraction at Solwara 1 can be measured.

  8. Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

    PubMed Central

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N.; Aslam, M.N.; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A.; Kilian, A.; Sharpe, Andrew G.; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  9. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).

    PubMed

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.

  10. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    PubMed

    Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.

  11. Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

    PubMed Central

    Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  12. Dioecy, more than monoecy, affects plant spatial genetic structure: the case study of Ficus

    PubMed Central

    Nazareno, Alison G; Alzate-Marin, Ana L; Pereira, Rodrigo Augusto S

    2013-01-01

    In this analysis, we attempt to understand how monoecy and dioecy drive spatial genetic structure (SGS) in plant populations. For this purpose, plants of the genus Ficus were used as a comparative model due to their particular characteristics, including high species diversity, variation in life histories, and sexual systems. One of the main issues we assessed is whether dioecious fig tree populations are more spatially genetically structured than monoecious populations. Using the Sp statistic, which allows for quantitative comparisons among different studies, we compared the extent of SGS between monoecious and dioecious Ficus species. To broaden our conclusions we used published data on an additional 27 monoecious and dioecious plant species. Furthermore, genetic diversity analyses were performed for two monoecious Ficus species using 12 microsatellite markers in order to strengthen our conclusions about SGS. Our results show that dioecy, more than monoecy, significantly contributes to SGS in plant populations. On average, the estimate of Sp was six times higher for dioecious Ficus species than monoecious Ficus species and it was two times higher in dioecious than monoecious plant species. Considering these results, we emphasize that the long-distance pollen dispersal mechanism in monoecious Ficus species seems to be the dominant factor in determining weak spatial genetic structure, high levels of genetic diversity, and lack of inbreeding. Although Ficus constitute a model species to study SGS, a more general comparison encompassing a wider range of plants is required in order to better understand how sexual systems affect genetic structure. PMID:24223285

  13. DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

    PubMed Central

    Borevitz, Justin O.

    2016-01-01

    DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon. Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species. PMID:27613611

  14. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications

    PubMed Central

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide. PMID:28107530

  15. Broad-Scale Genetic Diversity of Cannabis for Forensic Applications.

    PubMed

    Dufresnes, Christophe; Jan, Catherine; Bienert, Friederike; Goudet, Jérôme; Fumagalli, Luca

    2017-01-01

    Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the one hand, it represents a growing market for pharmaceutical and agricultural sectors. On the other hand, plants synthesizing the psychoactive THC produce the most widespread illicit drug in the world. Yet, the difficulty to reliably distinguish between Cannabis varieties based on morphological or biochemical criteria impedes the development of promising industrial programs and hinders the fight against narcotrafficking. Genetics offers an appropriate alternative to characterize drug vs. non-drug Cannabis. However, forensic applications require rapid and affordable genotyping of informative and reliable molecular markers for which a broad-scale reference database, representing both intra- and inter-variety variation, is available. Here we provide such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs) in 1 324 samples selected specifically for fibre (24 hemp varieties) and drug (15 marijuana varieties) production. We showed that these loci are sufficient to capture most of the genome-wide diversity patterns recently revealed by NGS data. We recovered strong genetic structure between marijuana and hemp and demonstrated that anonymous samples can be confidently assigned to either plant types. Fibres appear genetically homogeneous whereas drugs show low (often clonal) diversity within varieties, but very high genetic differentiation between them, likely resulting from breeding practices. Based on an additional test dataset including samples from 41 local police seizures, we showed that the genetic signature of marijuana cultivars could be used to trace crime scene evidence. To date, our study provides the most comprehensive genetic resource for Cannabis forensics worldwide.

  16. Genetic diversity of the giant tiger prawn Penaeus monodon in relation to trace metal pollution at the Tanzanian coast.

    PubMed

    Rumisha, Cyrus; Leermakers, Martine; Elskens, Marc; Mdegela, Robinson H; Gwakisa, Paul; Kochzius, Marc

    2017-01-30

    The genetic diversity of giant tiger prawns in relation to trace metals (TMs) pollution was analysed using 159 individuals from eight sites at the Tanzanian coast. The seven microsatellites analysed showed high degree of polymorphism (4-44 alleles). The measured genetic diversity (Ho=0.592±0.047) was comparable to that of populations in the Western Indian Ocean. Apart from that, correlation analysis revealed significant negative associations between genetic diversity and TMs pollution (p<0.05), supporting the genetic erosion hypothesis. Limited gene flow was indicated by a significant genetic differentiation (FST=0.059, p<0.05). The Mantel test rejected the isolation-by-distance hypothesis, but revealed that gene flow along the Tanzanian coast is limited by TMs pollution. This suggests that TMs affect larvae settlement and it may account for the measured deficiency of heterozygosity. This calls for strengthened pollution control measures in order to conserve this commercially important species.

  17. Two colonisation stages generate two different patterns of genetic diversity within native and invasive ranges of Ulex europaeus

    PubMed Central

    Hornoy, B; Atlan, A; Roussel, V; Buckley, Y M; Tarayre, M

    2013-01-01

    Genetic diversity and the way a species is introduced influence the capacity of populations of invasive species to persist in, and adapt to, their new environment. The diversity of introduced populations affects their evolutionary potential, which is particularly important for species that have invaded a wide range of habitats and climates, such as European gorse, Ulex europaeus. This species originated in the Iberian peninsula and colonised Europe in the Neolithic; over the course of the past two centuries it was introduced to, and has become invasive in, other continents. We characterised neutral genetic diversity and its structure in the native range and in invaded regions. By coupling these results with historical data, we have identified the way in which gorse populations were introduced and the consequences of introduction history on genetic diversity. Our study is based on the genotyping of individuals from 18 populations at six microsatellite loci. As U. europaeus is an allohexaploid species, we used recently developed tools that take into account genotypic ambiguity. Our results show that genetic diversity in gorse is very high and mainly contained within populations. We confirm that colonisation occurred in two stages. During the first stage, gorse spread out naturally from Spain towards northern Europe, losing some genetic diversity. During the second stage, gorse was introduced by humans into different regions of the world, from northern Europe. These introductions resulted in the loss of rare alleles but did not significantly reduce genetic diversity and thus the evolutionary potential of this invasive species. PMID:23759725

  18. Genetic diversity of Poa pratensis L. depending on geographical origin and compared with genetic markers

    PubMed Central

    Śmietana, Przemysław; Stępień, Edyta

    2016-01-01

    Background Poa pratensis is one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations of P. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation. Methods The molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA). Results The low value of Dice’s coefficient (0.369) along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin. Discussion The populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes of P. pratensis originating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability. PMID:27703847

  19. Genetic diversity and conservation of South African indigenous chicken populations.

    PubMed

    Mtileni, B J; Muchadeyi, F C; Maiwashe, A; Groeneveld, E; Groeneveld, L F; Dzama, K; Weigend, S

    2011-06-01

    In this study, we compare the level and distribution of genetic variation between South African conserved and village chicken populations using microsatellite markers. In addition, diversity in South African chickens was compared to that of a reference data set consisting of other African and purebred commercial lines. Three chicken populations Venda, Ovambo and Eastern Cape and four conserved flocks of the Venda, Ovambo, Naked Neck and Potchefstroom Koekoek from the Poultry Breeding Resource Unit of the Agricultural Research Council were genotyped at 29 autosomal microsatellite loci. All markers were polymorphic. Village chicken populations were more diverse than conservation flocks. structure software was used to cluster individuals to a predefined number of 2 ≤ K ≤ 6 clusters. The most probable clustering was found at K = 5 (95% identical runs). At this level of differentiation, the four conservation flocks separated as four independent clusters, while the three village chicken populations together formed another cluster. Thus, cluster analysis indicated a clear subdivision of each of the conservation flocks that were different from the three village chicken populations. The contribution of each South African chicken populations to the total diversity of the chickens studied was determined by calculating the optimal core set contributions based on Marker estimated kinship. Safe set analysis was carried out using bootstrapped kinship values calculated to relate the added genetic diversity of seven South African chicken populations to a set of reference populations consisting of other African and purebred commercial broiler and layer chickens. In both core set and the safe set analyses, village chicken populations scored slightly higher to the reference set compared to conservation flocks. Overall, the present study demonstrated that the conservation flocks of South African chickens displayed considerable genetic variability that is different from that of the

  20. Genetic diversity for wheat improvement as a conduit to food security

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity is paramount for any crops genetic improvement and this resides in three gene pools of the Triticeae for wheat. Access to the diversity and its exploitation is based upon genetic distance of the species relatives from the wheat genomes. Apart from the conventional genetic base fo...

  1. Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta)

    PubMed Central

    2012-01-01

    Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods). The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total) was found for Spirogyra (41 NHS) and for each clade (totaling 73 NHS). This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae. PMID:22655677

  2. A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

    EPA Science Inventory

    In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

  3. Genetic diversity despite population collapse in a critically endangered marine fish: the smalltooth sawfish (Pristis pectinata).

    PubMed

    Chapman, Demian D; Simpfendorfer, Colin A; Wiley, Tonya R; Poulakis, Gregg R; Curtis, Caitlin; Tringali, Michael; Carlson, John K; Feldheim, Kevin A

    2011-01-01

    Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.

  4. Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha).

    PubMed

    Tobias, Zachary J C; Yadav, Arun K; Schmidt-Rhaesa, Andreas; Poulin, Robert

    2017-03-09

    Hairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand: Gordius paranensis, Parachordodes diblastus and Euchordodes nigromaculatus. We also present genetic data on a previously reported but undescribed Gordius sp., as well as data from specimens of a new Gordionus sp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genus Gordionus and the potential for cryptic species within G. paranensis. Population-level analyses of E. nigromaculatus showed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host-parasite population co-structure in hairworms.

  5. Analytical DNA fingerprinting in lions: parentage, genetic diversity, and kinship.

    PubMed

    Gilbert, D A; Packer, C; Pusey, A E; Stephens, J C; O'Brien, S J

    1991-01-01

    The application of hypervariable minisatellite genomic families to the reconstruction of population genetic structure holds great promise in describing the demographic history and future prospects of free-ranging populations. This potential has not yet been realized due to unforeseen empirical constraints associated with the use of heterologous species probes, to theoretical limitations on the power of the procedure to track genic heterozygosity and kinship, and to the absence of extensive field studies to test genetic predictions. We combine here the technical development of feline-specific VNTR (variable number tandem repeat) families of genetic loci with the long-term demographic and behavioral observations of lion populations of the Serengeti ecosystem in East Africa. Minisatellite variation was used to quantify the extent of genetic variation in several populations that differed in their natural history and levels of inbreeding. Definitive parentage, both maternal and paternal, was assessed for 78 cubs born in 11 lion prides, permitting the assessment of precise genealogical relationships among some 200 lions. The extent of DNA restriction fragment sharing between lions was empirically calibrated with the coefficient of relatedness, r, in two different populations that had distinct demographic histories. The results suggest that reliable estimates of relative genetic diversity, of parentage, and of individual relatedness can be achieved in free-ranging populations, provided the minisatellite family is calibrated in established pedigrees for the species.

  6. Founder effects, inbreeding, and loss of genetic diversity in four avian reintroduction programs.

    PubMed

    Jamieson, Ian G

    2011-02-01

    The number of individuals translocated and released as part of a reintroduction is often small, as is the final established population, because the reintroduction site is typically small. Small founder and small resulting populations can result in population bottlenecks, which are associated with increased rates of inbreeding and loss of genetic diversity, both of which can affect the long-term viability of reintroduced populations. I used information derived from pedigrees of four monogamous bird species reintroduced onto two different islands (220 and 259 ha) in New Zealand to compare the pattern of inbreeding and loss of genetic diversity among the reintroduced populations. Although reintroduced populations founded with few individuals had higher levels of inbreeding, as predicted, other factors, including biased sex ratio and skewed breeding success, contributed to high levels of inbreeding and loss of genetic diversity. Of the 10-58 individuals released, 4-25 genetic founders contributed at least one living descendent and yielded approximately 3-11 founder-genome equivalents (number of genetic founders assuming an equal contribution of offspring and no random loss of alleles across generations) after seven breeding seasons. This range is much lower than the 20 founder-genome equivalents recommended for captive-bred populations. Although the level of inbreeding in one reintroduced population initially reached three times that of a closely related species, the long-term estimated rate of inbreeding of this one population was approximately one-third that of the other species due to differences in carrying capacities of the respective reintroduction sites. The increasing number of reintroductions to suitable areas that are smaller than those I examined here suggests that it might be useful to develop long-term strategies and guidelines for reintroduction programs, which would minimize inbreeding and maintain genetic diversity.

  7. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    PubMed

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

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago.

  8. Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea

    PubMed Central

    Lee, Dong Hwan; Kim, Jin-Beom; Lim, Jeong-A; Han, Sang-Wook; Heu, Sunggi

    2014-01-01

    The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed. PMID:25288994

  9. The effect of chromosome geometry on genetic diversity.

    PubMed

    Marri, Pradeep Reddy; Harris, Leigh K; Houmiel, Kathryn; Slater, Steven C; Ochman, Howard

    2008-05-01

    Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial taxa that possess different chromosome topologies. To test directly the contribution of chromosome architecture to genetic diversity and recombination, we examined sequence variation in strains of Agrobacterium Biovar 1, which are unique among sequenced bacteria in having both a circular and a linear chromosome. Whereas the allelic diversity among strains is generated principally by mutations, intragenic recombination is higher within genes situated on the circular chromosome. In contrast, recombination between genes is, on average, higher on the linear chromosome, but it occurs at the same rate as that observed between genes mapping to the distal portion of the circular chromosome. Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine.

  10. Origin, genetic diversity, and population structure of Chinese domestic sheep.

    PubMed

    Chen, Shan-Yuan; Duan, Zi-Yuan; Sha, Tao; Xiangyu, Jinggong; Wu, Shi-Fang; Zhang, Ya-Ping

    2006-07-19

    To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.

  11. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    PubMed Central

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

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

  12. Molecular markers: a potential resource for ginger genetic diversity studies.

    PubMed

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  13. Genetic diversity and relationships in populations of Bordetella spp.

    PubMed Central

    Musser, J M; Hewlett, E L; Peppler, M S; Selander, R K

    1986-01-01

    Genetic diversity in 60 strains of three nominal Bordetella species recovered from humans and other mammalian hosts was assessed by analyzing electrophoretically demonstrable allelic variation at structural genes encoding 15 enzymes. Eleven of the loci were polymorphic, and 14 distinctive electrophoretic types, representing multilocus genotypes, were identified. The population structure of Bordetella spp. is clonal, and genetic diversity is relatively limited compared with most other pathogenic bacteria and is insufficient to justify recognition of three species. All isolates of Bordetella parapertussis were of one electrophoretic type, which was closely similar to 9 of the 10 electrophoretic types represented by isolates of Bordetella bronchiseptica. Bordetella pertussis 18-323, which is used in mouse potency tests of vaccines, is more similar genetically to isolates of B. bronchiseptica and B. parapertussis than to other isolates currently assigned to the species B. pertussis. Apart from strain 18-323, the isolates of B. pertussis represented only two closely related clones, and all isolates of B. pertussis from North America (except strain 18-323) were genotypically identical. Strain Dejong, which has been classified as B. bronchiseptica, was strongly differentiated from all of the other Bordetella isolates examined. Images PMID:3957867

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

    PubMed Central

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

    2015-01-01

    Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes. PMID:25873150

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

    PubMed

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

    2015-01-01

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

  16. Factors affecting student performance in an undergraduate genetics course.

    PubMed

    Bormann, J Minick; Moser, D W; Bates, K E

    2013-05-01

    The objective of this study was to determine some of the factors that affect student success in a genetics course. Genetics for the Kansas State University College of Agriculture is taught in the Department of Animal Sciences and Industry and covers Mendelian inheritance, molecular genetics, and quantitative/population genetics. Data collected from 1,516 students over 7 yr included year and semester of the course; age; gender; state of residence; population of hometown; Kansas City metro resident or not; instructor of course; American College Testing Program (ACT) scores; number of transfer credits; major; college; preveterinary student or not; freshman, sophomore, junior, and senior grade point average (GPA); semester credits when taking genetics; class standing when enrolled in genetics; cumulative GPA before and after taking genetics; semester GPA in semester taking genetics, number of semesters between the biology prerequisite and genetics; grade in biology; location of biology course; and final percentage in genetics. Final percentage in genetics did not differ due to instructor, gender, state of residence, major, or college (P > 0.16). Transfer students tended to perform better than nontransfer students (P = 0.09), and students from the Kansas City metro outscored students from other areas (P = 0.03). Preveterinary option students scored higher in genetics than non-preveterinary students (P < 0.01). Seniors scored higher than juniors and sophomores, who scored higher than freshmen (P < 0.02). We observed a tendency for students with higher grades in biology to perform better in genetics (P = 0.06). Students who took biology at Kansas State University performed better in genetics than students who transferred the credit (P < 0.01). There was a negative regression of hometown population on score in genetics (P < 0.01), and positive regressions of ACT score, all measures of GPA, course load, and cumulative credits on final percentage in the course (P < 0.02). To

  17. Genetic diversity and connectivity of deep-sea hydrothermal vent metapopulations.

    PubMed

    Vrijenhoek, Robert C

    2010-10-01

    Deep-sea hydrothermal vents provide ephemeral habitats for animal communities that depend on chemosynthetic primary production. Sporadic volcanic and tectonic events destroy local vent fields and create new ones. Ongoing dispersal and cycles of extirpation and colonization affect the levels and distribution of genetic diversity in vent metapopulations. Several species exhibit evidence for stepping-stone dispersal along relatively linear, oceanic, ridge axes. Other species exhibit very high rates of gene flow, although natural barriers associated with variation in depth, deep-ocean currents, and lateral offsets of ridge axes often subdivide populations. Various degrees of impedance to dispersal across such boundaries are products of species-specific life histories and behaviours. Though unrelated to the size of a species range, levels of genetic diversity appear to correspond with the number of active vent localities that a species occupies within its range. Pioneer species that rapidly colonize nascent vents tend to be less subdivided and more diverse genetically than species that are slow to establish colonies at vents. Understanding the diversity and connectivity of vent metapopulations provides essential information for designing deep-sea preserves in regions that are under consideration for submarine mining of precious metals.

  18. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    PubMed

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    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.

  19. Effect of pollution on genetic diversity in the bay mussel Mytilus galloprovincialis and the acorn barnacle Balanus glandula.

    PubMed

    Ma, X L; Cowles, D L; Carter, R L

    2000-01-01

    To test if environmental contamination acts as a selection force affecting genetic diversity at the population level, two intertidal invertebrate species, Mytilus galloprovincialis and Balanus glandula, were collected from seven different bay sites in southern California. Collections were made at three relatively pristine 'clean' sites and four 'impacted' sites exposed to heavy industrial or boating activity, and which had previously been identified as having measurable levels of pollution. Genetic diversity at each site was assessed by comparing fragment polymorphisms generated from genomic DNA by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). All populations retained a large amount of genetic diversity and were genetically similar to each other. However, several different measures of diversity indicated that, for most primers, the populations of both species from impacted sites had lower genetic diversity compared to those populations from clean sites. Individuals at impacted sites were more likely to share the same haplotypes than were those from clean sites. Few bands seen in the clean sites were absent from the impacted sites or vice versa, but a number of bands in the clean site populations were significantly less common in the impacted populations, while a few bands uncommon in clean site populations were more common at impacted sites. Together, these results suggest that pollution at the impacted sites may reduce genetic diversity among the resident invertebrate populations.

  20. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    PubMed Central

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  1. Phylogenetic relationships, evolution, and genetic diversity of the domestic dog.

    PubMed

    Vilà, C; Maldonado, J E; Wayne, R K

    1999-01-01

    The spectacular diversity in size, conformation, and pelage that characterizes the domestic dog reflects not only the intensity of artificial selection but ultimately the genetic variability of founding populations. Here we review past molecular genetic data that are relevant to understanding the origin and phylogenetic relationships of the dog. DNA-DNA hybridization data show that the dog family Canidae diverged about 50 million years ago from other carnivore families. In contrast, the extant canids are very closely related and diverged from a common ancestor about 10 million years ago. The evidence supporting a close relationship of dogs with gray wolves is overwhelming. However, dogs are remarkably diverse in mitochondrial and nuclear genes. Mitochondrial DNA analysis suggests a more ancient origin of dogs than has been indicated by the fossil record. In addition, dogs have originated from or interbred with wolves throughout their history at different times and different places. We test the possibility of an independent domestication event in North America by analysis of mtDNA variation in the Xoloitzcuintli. This unusual breed is believed to have been kept isolated for thousands of years and may be one of the most ancient breeds in North America. Our results do not support a New World domestication of dogs nor a close association of the Xoloitzcuintli with other hair-less breeds of dogs. Despite their phenotypic uniformity, the Xoloitzcuintli has a surprisingly high level of mtDNA sequence variation. Other breeds are also genetically diverse, suggesting that dog breeds were often founded with a large number of dogs from outbred populations.

  2. Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.

    PubMed

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.

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

    PubMed Central

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

    2014-01-01

    Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool. PMID:24689851

  4. Paternal phylogeography and genetic diversity of East Asian goats.

    PubMed

    Waki, A; Sasazaki, S; Kobayashi, E; Mannen, H

    2015-06-01

    This study was a first analysis of paternal genetic diversity for extensive Asian domestic goats using SRY gene sequences. Sequencing comparison of the SRY 3'-untranslated region among 210 Asian goats revealed four haplotypes (Y1A, Y1B, Y2A and Y2B) derived from four variable sites including a novel substitution detected in this study. In Asian goats, the predominant haplotype was Y1A (62%) and second most common was Y2B (30%). Interestingly, the Y2B was a unique East Asian Y chromosomal variant, which differentiates eastern and western Eurasian goats. The SRY geographic distribution in Myanmar and Cambodia indicated predominant the haplotype Y1A in plains areas and a high frequency of Y2B in mountain areas. The results suggest recent genetic infiltration of modern breeds into South-East Asian goats and an ancestral SRY Y2B haplotype in Asian native goats.

  5. The benefits of genetic diversity outweigh those of kin association in a territorial animal.

    PubMed

    Griffiths, S W; Armstrong, J D

    2001-06-22

    The theories of kin selection and heterogeneous advantage have been central to studies of altruistic behaviour and the evolution of sex over the last 35 years. Yet they predict diametrically opposite effects of genetic diversity on population density. Close relatives gain inclusive fitness advantages by preferentially associating with and behaving altruistically towards one another. However, heterogeneous advantage, which predicts competition to be highest when genetic diversity is low, suggests that benefits will be greater for individuals in groups of non-kin. Here we test how these two processes balance and affect the productivity of populations of animals in natural habitats. We report from a study of juvenile Atlantic salmon in the wild that heterogeneous advantage outweighs the benefits of kin-biased behaviour, resulting in a 1.8-fold higher population biomass and significantly better condition of individual fish.

  6. Genetic diversity of Argentine isolates of feline immunodeficiency virus.

    PubMed

    Pecoraro, M R; Tomonaga, K; Miyazawa, T; Kawaguchi, Y; Sugita, S; Tohya, Y; Kai, C; Etcheverrigaray, M E; Mikami, T

    1996-09-01

    We report the nucleotide sequence and genetic diversity of part of the envelope (env) gene of four strains of feline immunodeficiency virus (FIV) isolated from Argentine domestic cats. The DNA encoding the V3 to V5 regions of the env gene of the FIV isolates were amplified by PCR, cloned and sequenced. Phylogenetic analysis revealed that the Argentine isolates did not cluster into a single group; one isolate clustered with subtype B FIV isolated in the USA and Japan, whereas the others formed a new cluster of FIV which might represent a prototype sequence for subtype E.

  7. Genetic diversity of Neisseria lactamica strains from epidemiologically defined carriers.

    PubMed

    Alber, D; Oberkötter, M; Suerbaum, S; Claus, H; Frosch, M; Vogel, U

    2001-05-01

    We assessed the genetic diversity of 26 Neisseria lactamica strains from epidemiologically related sources, i.e., groups of kindergartens and primary schools in three Bavarian towns, by the partial sequencing of the argF, rho, recA, and 16S ribosomal genes. We found a total of 17 genotypes, of which 12 were found only in one strain. The genotypes comprised 5 alleles of the argF gene, 9 of rho, 8 of recA, and 10 of the 16S ribosomal DNA. Sequence analysis by determination of homoplasy ratios and split decomposition analysis revealed abundant recombination within N. lactamica.

  8. Genetic diversity of Eurycoma longifolia inferred from single nucleotide polymorphisms.

    PubMed

    Osman, Asiah; Jordan, Barbara; Lessard, Philip A; Muhammad, Norwati; Haron, M Rosli; Riffin, Norifiza Mat; Sinskey, Anthony J; Rha, ChoKyun; Housman, David E

    2003-03-01

    Eurycoma longifolia Jack. is a treelet that grows in the forests of Southeast Asia and is widely used throughout the region because of its reported medicinal properties. Widespread harvesting of wild-grown trees has led to rapid thinning of natural populations, causing a potential decrease in genetic diversity among E. longifolia. Suitable genetic markers would be very useful for propagation and breeding programs to support conservation of this species, although no such markers currently exist. To meet this need, we have applied a genome complexity reduction strategy to identify a series of single nucleotide polymorphisms (SNPs) within the genomes of several E. longifolia accessions. We have found that the occurrence of these SNPs reflects the geographic origins of individual plants and can distinguish different natural populations. This work demonstrates the rapid development of molecular genetic markers in species for which little or no genomic sequence information is available. The SNP markers that we have developed in this study will also be useful for identifying genetic fingerprints that correlate with other properties of E. longifolia, such as high regenerability or the appearance of bioactive metabolites.

  9. Centennial olive trees as a reservoir of genetic diversity

    PubMed Central

    Díez, Concepción M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

    2011-01-01

    Background and Aims Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. Methods The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Key Results Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. Conclusions This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity. PMID:21852276

  10. Inter simple sequence repeat (ISSR) analysis of genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

    PubMed

    Assefa, Kebebew; Merker, Arnulf; Tefera, Hailu

    2003-01-01

    The DNA polymorphism among 92 selected tef genotypes belonging to eight origin groups was assessed using eight inter simple sequence repeat (ISSR) primers. The objectives were to examine the possibility of using ISSR markers for unravelling genetic diversity in tef, and to assess the extent and pattern of genetic diversity in the test germplasm with respect to origin groups. The eight primers were able to separate or distinguish all of the 92 tef genotypes based on a total of 110 polymorphic bands among the test lines. The Jaccard similarity coefficient among the test genotypes ranged from 0.26 to 0.86, and at about 60 % similarity level the clustering of this matrix using the unweighted pair-group method based on arithmetic average (UPGMA) resulted in the formation of six major clusters of 2 to 37 lines with further eight lines remaining ungrouped. The standardized Nei genetic distance among the eight groups of origin ranged between 0.03 and 0.32. The UPGMA clustering using the standardized genetic distance matrix resulted in the identification of three clusters of the eight groups of origin with bootstrap values ranging from 56 to 97. The overall mean Shannon Weaver diversity index of the test lines was 0.73, indicating better resolution of genetic diversity in tef with ISSR markers than with phenotypic (morphological) traits used in previous studies. This can be attributed mainly to the larger number of loci generated for evaluation with ISSR analysis as compared to the few number of phenotypic traits amenable for assessment and which are further greatly affected by environment and genotype x environment interaction. Analysis of variance of mean Shannon Weaver diversity indices revealed substantial (P < or = 0.05) variation in the level of diversity among the eight groups of origin. In conclusion, our results indicate that ISSR can be useful as DNA-based molecular markers for studying genetic diversity and phylogenetic relationships, DNA fingerprinting for the

  11. How spatio-temporal habitat connectivity affects amphibian genetic structure

    PubMed Central

    Watts, Alexander G.; Schlichting, Peter E.; Billerman, Shawn M.; Jesmer, Brett R.; Micheletti, Steven; Fortin, Marie-Josée; Funk, W. Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A.

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations. PMID:26442094

  12. How spatio-temporal habitat connectivity affects amphibian genetic structure

    USGS Publications Warehouse

    Watts, Alexander G.; Schlichting, P; Billerman, S; Jesmer, B; Micheletti, S; Fortin, M.-J.; Funk, W.C.; Hapeman, P; Muths, Erin L.; Murphy, M.A.

    2015-01-01

    Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

  13. Males and females contribute unequally to offspring genetic diversity in the polygynandrous mating system of wild boar.

    PubMed

    Pérez-González, Javier; Costa, Vânia; Santos, Pedro; Slate, Jon; Carranza, Juan; Fernández-Llario, Pedro; Zsolnai, Attila; Monteiro, Nuno M; Anton, István; Buzgó, József; Varga, Gyula; Beja-Pereira, Albano

    2014-01-01

    The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa) has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation.

  14. Males and Females Contribute Unequally to Offspring Genetic Diversity in the Polygynandrous Mating System of Wild Boar

    PubMed Central

    Pérez-González, Javier; Costa, Vânia; Santos, Pedro; Slate, Jon; Carranza, Juan; Fernández-Llario, Pedro; Zsolnai, Attila; Monteiro, Nuno M.; Anton, István; Buzgó, József; Varga, Gyula; Beja-Pereira, Albano

    2014-01-01

    The maintenance of genetic diversity across generations depends on both the number of reproducing males and females. Variance in reproductive success, multiple paternity and litter size can all affect the relative contributions of male and female parents to genetic variation of progeny. The mating system of the wild boar (Sus scrofa) has been described as polygynous, although evidence of multiple paternity in litters has been found. Using 14 microsatellite markers, we evaluated the contribution of males and females to genetic variation in the next generation in independent wild boar populations from the Iberian Peninsula and Hungary. Genetic contributions of males and females were obtained by distinguishing the paternal and maternal genetic component inherited by the progeny. We found that the paternally inherited genetic component of progeny was more diverse than the maternally inherited component. Simulations showed that this finding might be due to a sampling bias. However, after controlling for the bias by fitting both the genetic diversity in the adult population and the number of reproductive individuals in the models, paternally inherited genotypes remained more diverse than those inherited maternally. Our results suggest new insights into how promiscuous mating systems can help maintain genetic variation. PMID:25541986

  15. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.

    PubMed

    Lohmueller, Kirk E; Albrechtsen, Anders; Li, Yingrui; Kim, Su Yeon; Korneliussen, Thorfinn; Vinckenbosch, Nicolas; Tian, Geng; Huerta-Sanchez, Emilia; Feder, Alison F; Grarup, Niels; Jørgensen, Torben; Jiang, Tao; Witte, Daniel R; Sandbæk, Annelli; Hellmann, Ines; Lauritzen, Torsten; Hansen, Torben; Pedersen, Oluf; Wang, Jun; Nielsen, Rasmus

    2011-10-01

    A major question in evolutionary biology is how natural selection has shaped patterns of genetic variation across the human genome. Previous work has documented a reduction in genetic diversity in regions of the genome with low recombination rates. However, it is unclear whether other summaries of genetic variation, like allele frequencies, are also correlated with recombination rate and whether these correlations can be explained solely by negative selection against deleterious mutations or whether positive selection acting on favorable alleles is also required. Here we attempt to address these questions by analyzing three different genome-wide resequencing datasets from European individuals. We document several significant correlations between different genomic features. In particular, we find that average minor allele frequency and diversity are reduced in regions of low recombination and that human diversity, human-chimp divergence, and average minor allele frequency are reduced near genes. Population genetic simulations show that either positive natural selection acting on favorable mutations or negative natural selection acting against deleterious mutations can explain these correlations. However, models with strong positive selection on nonsynonymous mutations and little negative selection predict a stronger negative correlation between neutral diversity and nonsynonymous divergence than observed in the actual data, supporting the importance of negative, rather than positive, selection throughout the genome. Further, we show that the widespread presence of weakly deleterious alleles, rather than a small number of strongly positively selected mutations, is responsible for the correlation between neutral genetic diversity and recombination rate. This work suggests that natural selection has affected multiple aspects of linked neutral variation throughout the human genome and that positive selection is not required to explain these observations.

  16. Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change.

    PubMed

    Wan, Jizhong; Wang, Chunjing; Yu, Jinghua; Nie, Siming; Han, Shijie; Zu, Yuangang; Chen, Changmei; Yuan, Shusheng; Wang, Qinggui

    2014-07-01

    Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangered due to excessive and illegal harvesting for use in Chinese medicine. Here, we test a general computational method for the prediction of priority conservation areas (PCAs) by measuring the genetic diversity of P. amurense across the entirety of northeast China using a single strand repeat analysis of twenty microsatellite markers. Using computational modeling, we evaluated the geographical distribution of the species, both now and in different future climate change scenarios. Different populations were analyzed according to genetic diversity, and PCAs were identified using a spatial conservation prioritization framework. These conservation areas were optimized to account for the geographical distribution of P. amurense both now and in the future, to effectively promote gene flow, and to have a long period of validity. In situ and ex situ conservation, strategies for vulnerable populations were proposed. Three populations with low genetic diversity are predicted to be negatively affected by climate change, making conservation of genetic diversity challenging due to decreasing habitat suitability. Habitat suitability was important for the assessment of genetic variability in existing nature reserves, which were found to be much smaller than the proposed PCAs. Finally, a simple set of conservation measures was established through modeling. This combined molecular and computational ecology approach provides a framework for planning the protection of species endangered by climate

  17. Model-based conservation planning of the genetic diversity of Phellodendron amurense Rupr due to climate change

    PubMed Central

    Wan, Jizhong; Wang, Chunjing; Yu, Jinghua; Nie, Siming; Han, Shijie; Zu, Yuangang; Chen, Changmei; Yuan, Shusheng; Wang, Qinggui

    2014-01-01

    Climate change affects both habitat suitability and the genetic diversity of wild plants. Therefore, predicting and establishing the most effective and coherent conservation areas is essential for the conservation of genetic diversity in response to climate change. This is because genetic variance is a product not only of habitat suitability in conservation areas but also of efficient protection and management. Phellodendron amurense Rupr. is a tree species (family Rutaceae) that is endangered due to excessive and illegal harvesting for use in Chinese medicine. Here, we test a general computational method for the prediction of priority conservation areas (PCAs) by measuring the genetic diversity of P. amurense across the entirety of northeast China using a single strand repeat analysis of twenty microsatellite markers. Using computational modeling, we evaluated the geographical distribution of the species, both now and in different future climate change scenarios. Different populations were analyzed according to genetic diversity, and PCAs were identified using a spatial conservation prioritization framework. These conservation areas were optimized to account for the geographical distribution of P. amurense both now and in the future, to effectively promote gene flow, and to have a long period of validity. In situ and ex situ conservation, strategies for vulnerable populations were proposed. Three populations with low genetic diversity are predicted to be negatively affected by climate change, making conservation of genetic diversity challenging due to decreasing habitat suitability. Habitat suitability was important for the assessment of genetic variability in existing nature reserves, which were found to be much smaller than the proposed PCAs. Finally, a simple set of conservation measures was established through modeling. This combined molecular and computational ecology approach provides a framework for planning the protection of species endangered by climate

  18. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    PubMed Central

    Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

    2001-01-01

    Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

  19. Genetic diversity in the SIR model of pathogen evolution.

    PubMed

    Gordo, Isabel; Gomes, M Gabriela M; Reis, Daniel G; Campos, Paulo R A

    2009-01-01

    We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0)(1+s)) is higher than the fitness of the resident strain (R(0)). We show that this invasion probability is given by the relative increment in R(0) of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  20. Genetic diversity in a world germplasm collection of tall fescue

    PubMed Central

    Cuyeu, Romina; Rosso, Beatriz; Pagano, Elba; Soto, Gabriela; Fox, Romina; Ayub, Nicolás Daniel

    2013-01-01

    Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs. PMID:23885206

  1. Insights into Penicillium roqueforti Morphological and Genetic Diversity.

    PubMed

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection.

  2. Insights into Penicillium roqueforti Morphological and Genetic Diversity

    PubMed Central

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection. PMID:26091176

  3. Genotypic and Phenotypic Diversity Does Not Affect Productivity and Drought Response in Competitive Stands of Trifolium repens.

    PubMed

    Huber, Heidrun; During, Heinjo J; Bruine de Bruin, Fabienne; Vermeulen, Peter J; Anten, Niels P R

    2016-01-01

    Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning. We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets) were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions. Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly affected by soil

  4. Characterisation of the genetic diversity of Brucella by multilocus sequencing

    PubMed Central

    Whatmore, Adrian M; Perrett, Lorraine L; MacMillan, Alastair P

    2007-01-01

    Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs). Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially <1. Analysis of linkage equilibrium between loci indicated a strongly clonal overall population structure. Concatenated sequence data were used to construct an unrooted neighbour-joining tree representing the relationships between STs. This shows that four previously characterized classical Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing

  5. GENETIC DIVERSITY, PARENTAGE VERIFICATION AND GENETIC BOTTLENECKS EVALUATION IN IRANIAN TURKMEN HORSE BREED.

    PubMed

    Rahimi-Mianji, G; Nejati-Javaremi, A; Farhadi, A

    2015-09-01

    The present study was undertaken to genetically evaluate Turkmen horses for genetic diversity and to evaluate whether they have experienced any recent genetic bottlenecks. A total of 565 individuals from Turkmen horses were characterized for within breed diversity using 12 microsatellite markers. The estimated mean allelic diversity was (9.42 ± 1.78) per locus, with a total of 131 alleles in genotyped samples. A high level of genetic variability within this breed was observed in terms of high values of effective number of alleles (4.70 ± 1.36), observed heterozygosity (0.757 ± 0.19), expected Nei's heterozygosity (0.765 ± 0.13), and polymorphism information content (0.776 ± 0.17). The estimated cumulative probability of exclusion of wrongly named parents (PE) was high, with an average value of 99.96% that indicates the effectiveness of applied markers in resolving of parentage typing in Turkmen horse population. The paternity testing results did not show any misidentification and all selected animals were qualified based on genotypic information using a likelihood-based method. Low values of Wright's fixation index, F(IS) (0.012) indicated low levels of inbreeding. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon sign rank test suggested that Turkmen horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal 'L' shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent past history of this breed. Further research work should be carrying out to clarify the cause of discrepancy observed forbottleneck results in this breed. In conclusion, despite unplanned breeding in Turkmen horse population, this breed still has sufficient genetic variability and could provide a valuable source of genetic material that may use for meeting the demands of future breeding programs.

  6. The loss of genetic diversity in Sichuan taimen as revealed by DNA fingerprinting.

    PubMed

    Wu, Xue-Chang

    2006-06-01

    Species endangerment often derives from the "endangerment" of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during 1998-1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity.

  7. Genetic diversity, linkage disequilibrium, and genome evolution in a soft winter wheat population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding genetic diversity within a crop is fundamental to its efficient exploitation. The advent of new high-throughput marker systems offers the opportunity to expand the scope and depth of our investigation of diversity. Our objectives were to analyze the genetic diversity of two populatio...

  8. Parallel responses of species and genetic diversity to El Niño Southern Oscillation-induced environmental destruction.

    PubMed

    Cleary, Daniel F R; Fauvelot, Cécile; Genner, Martin J; Menken, Steph B J; Mooers, Arne Ø

    2006-03-01

    Species diversity within communities and genetic diversity within species are two fundamental levels of biodiversity. Positive relationships between species richness and within-species genetic diversity have recently been documented across natural and semi-natural habitat islands, leading Vellend to suggest a novel macro-ecological pattern termed the species-genetic diversity correlation. We tested whether this prediction holds for areas affected by recent habitat disturbance using butterfly communities in east Kalimantan, Indonesia. Here, we show that both strong spatial and temporal correlations exist between species and allelic richness across rainforest habitats affected by El Niño Southern Oscillation-induced disturbance. Coupled with evidence that changes in species richness are a direct result of local extirpation and lower recruitment, these data suggest that forces governing variation at the two levels operate over parallel and short timescales, with implications for biodiversity recovery following disturbance. Remnant communities may be doubly affected, with reductions in species richness being associated with reductions in genetic diversity within remnant species.

  9. Yeast Diversity and Persistence in Botrytis-Affected Wine Fermentations

    PubMed Central

    Mills, David A.; Johannsen, Eric A.; Cocolin, Luca

    2002-01-01

    Culture-dependent and -independent methods were used to examine the yeast diversity present in botrytis-affected (“botrytized”) wine fermentations carried out at high (∼30°C) and ambient (∼20°C) temperatures. Fermentations at both temperatures possessed similar populations of Saccharomyces, Hanseniaspora, Pichia, Metschnikowia, Kluyveromyces, and Candida species. However, higher populations of non-Saccharomyces yeasts persisted in ambient-temperature fermentations, with Candida and, to a lesser extent, Kluyveromyces species remaining long after the fermentation was dominated by Saccharomyces. In general, denaturing gradient gel electrophoresis profiles of yeast ribosomal DNA or rRNA amplified from the fermentation samples correlated well with the plating data. The direct molecular methods also revealed a Hanseniaspora osmophila population not identified in the plating analysis. rRNA analysis also indicated a large population (>106 cells per ml) of a nonculturable Candida strain in the high-temperature fermentation. Monoculture analysis of the Candida isolate indicated an extreme fructophilic phenotype and correlated with an increased glucose/fructose ratio in fermentations containing higher populations of Candida. Analysis of wine fermentation microbial ecology by using both culture-dependent and -independent methods reveals the complexity of yeast interactions enriched during spontaneous fermentations. PMID:12324335

  10. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter

    PubMed Central

    Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

    2015-01-01

    Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding. PMID:25859251

  11. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

    PubMed

    Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

    2015-01-01

    Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding.

  12. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

    PubMed Central

    Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P.; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

    2016-01-01

    The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR. PMID:26915094

  13. Population genetic analysis of Giardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources.

    PubMed

    Durigan, Mauricio; Ciampi-Guillardi, Maisa; Rodrigues, Ricardo C A; Greinert-Goulart, Juliane A; Siqueira-Castro, Isabel C V; Leal, Diego A G; Yamashiro, Sandra; Bonatti, Taís R; Zucchi, Maria I; Franco, Regina M B; de Souza, Anete P

    2017-01-11

    Giardia duodenalis is a flagellated intestinal protozoan responsible for infections in various hosts including humans and several wild and domestic animals. Few studies have correlated environmental contamination and clinical infections in the same region. The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses to verify haplotype sharing and the degree of genetic similarity among populations from clinical and environmental sources in the metropolitan region of Campinas. The results showed high diversity of haplotypes and substantial genetic similarity between clinical and environmental groups of G. duodenalis. We demonstrated sharing of Giardia genotypes among the different populations studied. The comparison between veterinary and human sequences led us to identify new zoonotic genotypes, including human isolates from genetic assemblage C. The application of a population genetic analysis in epidemiological studies allows quantification of the degree of genetic similarity among populations of Giardia duodenalis from different sources of contamination. The genetic similarity of Giardia isolates among human, veterinary, and environmental groups reinforced the correlation between clinical and environmental isolates in this region, which is of great importance for public health.

  14. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum.

    PubMed

    Stewart, Jane E; Brooks, Kyle; Brannen, Phillip M; Cline, William O; Brewer, Marin T

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

  15. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum

    PubMed Central

    Stewart, Jane E.; Brooks, Kyle; Brannen, Phillip M.; Cline, William O.; Brewer, Marin T.

    2015-01-01

    Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population

  16. Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

  17. Population size and time since island isolation determine genetic diversity loss in insular frog populations.

    PubMed

    Wang, Supen; Zhu, Wei; Gao, Xu; Li, Xianping; Yan, Shaofei; Liu, Xuan; Yang, Ji; Gao, Zengxiang; Li, Yiming

    2014-02-01

    Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used nine microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square-root-transformed) and population size (log-transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations.

  18. Genetic diversity and floral width variation in introduced and native populations of a long-lived woody perennial

    PubMed Central

    Stout, Jane C.; Duffy, Karl J.; Egan, Paul A.; Harbourne, Maeve; Hodkinson, Trevor R.

    2015-01-01

    Populations of introduced species in their new environments are expected to differ from native populations, due to processes such as genetic drift, founder effects and local adaptation, which can often result in rapid phenotypic change. Such processes can also lead to changes in the genetic structure of these populations. This study investigated the populations of Rhododendron ponticum in its introduced range in Ireland, where it is severely invasive, to determine both genetic and flower width diversity and differentiation. We compared six introduced Irish populations with two populations from R. ponticum's native range in Spain, using amplified fragment length polymorphism and simple sequence repeat genetic markers. We measured flower width, a trait that may affect pollinator visitation, from four Irish and four Spanish populations by measuring both the width at the corolla tip and tube base (nectar holder width). With both genetic markers, populations were differentiated between Ireland and Spain and from each other in both countries. However, populations displayed low genetic diversity (mean Nei's genetic diversity = 0.22), with the largest proportion (76–93 %) of genetic variation contained within, rather than between, populations. Although corolla width was highly variable between individuals within populations, tube width was significantly wider (>0.5 mm) in introduced, compared with native, populations. Our results show that the same species can have genetically distinct populations in both invasive and native regions, and that differences in floral width may occur, possibly in response to ecological sorting processes or local adaptation to pollinator communities. PMID:25527475

  19. Genetic diversity of Plasmodium vivax isolates from Azerbaijan

    PubMed Central

    Leclerc, Marie Claude; Menegon, Michela; Cligny, Alexandra; Noyer, Jean Louis; Mammadov, Suleyman; Aliyev, Namig; Gasimov, Elkhan; Majori, Giancarlo; Severini, Carlo

    2004-01-01

    Background Plasmodium vivax, although causing a less serious disease than Plasmodium falciparum, is the most widespread of the four human malarial species. Further to the recent recrudescence of P. vivax cases in the Newly Independent States (NIS) of central Asia, a survey on the genetic diversity and dissemination in Azerbaijan was undertaken. Azerbaijan is at the crossroads of Asia and, as such, could see a rise in the number of cases, although an effective malaria control programme has been established in the country. Methods Thirty-six P. vivax isolates from Central Azerbaijan were characterized by analysing the genetic polymorphism of the circumsporozoite protein (CSP) and the merozoite surface protein 1 (MSP-1) genes, using PCR amplifications and amplicons sequencing. Results Analysis of CSP sequences showed that all the processed isolates belong to the VK 210 type, with variations in the alternation of alanine residue (A) or aspartic acid residue (D) in the repeat motif GDRA(A/D)GQPA along the sequence. As far as MSP-1 genotyping is concerned, it was found that the majority of isolates analysed belong to Belem and Sal I types. Five recombinant isolates were also identified. Combined analysis with the two genetic markers allowed the identification of 19 plasmodial sub-types. Conclusion The results obtained in the present study indicate that there are several P. vivax clones circulating in Azerbaijan and, consequently, a careful malaria surveillance could be of paramount importance to identify, at early stage, the occurrence of possible P. vivax malaria outbreaks. PMID:15535878

  20. The Nuclear DNA Content and Genetic Diversity of Lampetra morii

    PubMed Central

    Yan, Xinyu; Meng, Wenbin; Wu, Fenfang; Xu, Anlong; Chen, Shangwu; Huang, Shengfeng

    2016-01-01

    We investigated the nuclear DNA content and genetic diversity of a river lamprey, the Korean lamprey Lampetra morii, which is distributed in the northeast of China. L. morii spends its whole life cycle in fresh water, and its adult size is relatively small (~160 mm long) compared with that of other lampreys. The haploid nuclear DNA content of L. morii is 1.618 pg (approximately 1.582 Gb) in germline cells, and there is ~15% germline DNA loss in somatic cells. These values are significantly smaller than those of Petromyzon marinus, a lamprey with a published draft genome. The chromosomes of L. morii are small and acrocentric, with a diploid modal number of 2n = 132, lower than some other lampreys. Sequence and AFLP analyses suggest that the allelic polymorphism rate (~0.14% based on examined nuclear and mitochondrial DNA sequences) of L. morii is much lower than that (~2%) of P. marinus. Phylogenetic analysis based on a mitochondrial DNA fragment confirms that L. morii belongs to the genus Lampetra, which, together with the genus Lethenteron, forms a sister group to P. marinus. These genetic background data are valuable for subsequent genetic and genomic research on L. morii. PMID:27388621

  1. Analysis of genetic diversity of Fusarium tupiense, the main causal agent of mango malformation disease in southern Spain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mango malformation disease (MMD) has become an important global disease affecting this crop. The aim of this study was to identify the main causal agents of MMD in the Axarquía region of southern Spain and determine their genetic diversity. Fusarium mangiferae was previously described in the Axarquí...

  2. [Genetic diversity of microsatellite loci in captive Amur tigers].

    PubMed

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten

  3. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping.

    PubMed

    Jin, Liang; Lu, Yan; Xiao, Peng; Sun, Mei; Corke, Harold; Bao, Jinsong

    2010-08-01

    Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify

  4. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

    PubMed

    Taberlet, Pierre; Zimmermann, Niklaus E; Englisch, Thorsten; Tribsch, Andreas; Holderegger, Rolf; Alvarez, Nadir; Niklfeld, Harald; Coldea, Gheorghe; Mirek, Zbigniew; Moilanen, Atte; Ahlmer, Wolfgang; Marsan, Paolo Ajmone; Bona, Enzo; Bovio, Maurizio; Choler, Philippe; Cieślak, Elżbieta; Colli, Licia; Cristea, Vasile; Dalmas, Jean-Pierre; Frajman, Božo; Garraud, Luc; Gaudeul, Myriam; Gielly, Ludovic; Gutermann, Walter; Jogan, Nejc; Kagalo, Alexander A; Korbecka, Grażyna; Küpfer, Philippe; Lequette, Benoît; Letz, Dominik Roman; Manel, Stéphanie; Mansion, Guilhem; Marhold, Karol; Martini, Fabrizio; Negrini, Riccardo; Niño, Fernando; Paun, Ovidiu; Pellecchia, Marco; Perico, Giovanni; Piękoś-Mirkowa, Halina; Prosser, Filippo; Puşcaş, Mihai; Ronikier, Michał; Scheuerer, Martin; Schneeweiss, Gerald M; Schönswetter, Peter; Schratt-Ehrendorfer, Luise; Schüpfer, Fanny; Selvaggi, Alberto; Steinmann, Katharina; Thiel-Egenter, Conny; van Loo, Marcela; Winkler, Manuela; Wohlgemuth, Thomas; Wraber, Tone; Gugerli, Felix; Vellend, Mark

    2012-12-01

    The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.

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

    PubMed Central

    de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

    2013-01-01

    Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings. PMID:23569417

  6. Genetic and Biological Diversity of Trichoderma stromaticum, a Mycoparasite of the Cacao Witches'-Broom Pathogen.

    PubMed

    de Souza, Jorge T; Pomella, Alan W V; Bowers, John H; Pirovani, Carlos P; Loguercio, Leandro L; Hebbar, K Prakash

    2006-01-01

    ABSTRACT The witches'-broom disease, caused by the basidiomycete Crinipellis perniciosa, is the most limiting factor for cacao cultivation in Brazil. Trichoderma stromaticum is a mycoparasite of the witches'-broom pathogen of cacao that is currently being applied in the field to manage the disease in Bahia State, Brazil. In this work, molecular and traditional methods were used to study the genetic and biological diversity of this mycoparasite. Ninety-one isolates, mostly collected from farms not sprayed with the fungus, were analyzed by amplified fragment length polymorphisms (AFLP), which showed that two genetic groups (I and II) of T. stromaticum occur in Bahia State. This classification of T. stromaticum into two distinct AFLP groups was also in agreement with several other characteristics, including growth on agar media at different temperatures and sporulation on infected stem segments (broom pieces) and rice grains. Group II favors higher temperatures compared with group I. The genetic and biological differences of the isolates, however, were not evident in field experiments, where sporulation was evaluated on the surface of brooms under natural conditions. Our results show that there is considerable genetic and biological diversity within T. stromaticum in Bahia and other cacao-growing regions of South America that are affected by the witches'-broom disease. This diversity could be explored in the development of efficient biological control agents against the disease. Factors that may affect the application and performance of this biocontrol agent in the field, such as sporulation on rice substrate and on the brooms and growth at various temperatures, are discussed.

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

    PubMed

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

    2017-01-01

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

  8. Effect of subtherapeutic antimicrobials on genetic diversity of Enterococcus faecium from chickens.

    PubMed

    Jackson, Charlene R; Debnam, Antoinette L; Avellaneda, Gloria E; Barrett, John B; Hofacre, Charles L

    2006-03-01

    The effect of growth promotants (bacitracin, virginiamycin, and flavomycin) on the genetic population of Enterococcusfaecium isolated from a commercially integrated poultry farm was examined. A total of 551 E. faecium were isolated from chick boxliners (n=16), litter (n=334), feed (n=67), and carcass rinse (n=134) samples from four chicken houses. Two houses on the farm were control houses and did not use any antimicrobials while two other houses on the farm used flavomycin, virginiamycin, and bacitracin during six different chicken grow outs. BOX-PCR and pulsed-field gel electrophoresis (PFGE) results indicated that E. faecium strains had a high degree of genetic diversity as overall clustering was independent of source, house, or grow out. Similarity of > or =60% for the majority of BOX-PCR genogroups and > or =80% for the majority of PFGE genogroups was observed for a subset of carcass rinse samples (n=45) examined. Seventy-nine percent (19/24) of isolates in BOX-PCR genogroup 2 also clustered in PFGE genogroup 2, although no association between the isolates and house or grow out was observed. These results suggest that E. faecium from chicken are genetically diverse and that growth-promoting antimicrobials do not affect the genetic population of E. faecium.

  9. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure

    PubMed Central

    De Luca, Daniele; Catanese, Gaetano; Procaccini, Gabriele; Fiorito, Graziano

    2016-01-01

    The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective. PMID:26881847

  10. Octopus vulgaris (Cuvier, 1797) in the Mediterranean Sea: Genetic Diversity and Population Structure.

    PubMed

    De Luca, Daniele; Catanese, Gaetano; Procaccini, Gabriele; Fiorito, Graziano

    2016-01-01

    The common octopus, Octopus vulgaris Cuvier 1797, is a largely exploited cephalopod species in the Mediterranean Sea and the Atlantic Ocean, as well as along the coasts of Africa, Brazil and Japan, where its taxonomic identity is still debated. The assessment of its genetic structure is a pressing need to correctly manage the resource and to avoid overfishing and collapsing of local stocks. Here we analysed genetic variation and population structure of O. vulgaris using thirteen microsatellite loci in seven sampling localities from the Mediterranean Sea and one from the Atlantic Ocean. We also used a DNA barcoding approach by COI gene fragment to understand the phylogenetic relationships among the specimens here investigated and the ones whose sequences are available in literature. Our results reveal high levels of allelic richness and moderate heterozygosity in all samples investigated, and a pronounced differentiation of the Atlantic and Sicilian specimens. This latter aspect seems to support the isolation of the biota within the Strait of Messina. A certain degree of differentiation was detected among the other geographic samples within the Mediterranean Sea, which is more compatible with an island model than isolation by distance. The occurrence of null alleles affected more genetic diversity indices than population structure estimations. This study provides new insights about the genetic diversity and structure of O. vulgaris in the area of interest, which can be used as guidelines for a fisheries management perspective.

  11. Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans.

    PubMed

    Valliyodan, Babu; Ye, Heng; Song, Li; Murphy, MacKensie; Shannon, J Grover; Nguyen, Henry T

    2016-12-07

    Drought and its interaction with high temperature are the major abiotic stress factors affecting soybean yield and production stability. Ongoing climate changes are anticipated to intensify drought events, which will further impact crop production and food security. However, excessive water also limits soybean production. The success of soybean breeding programmes for crop improvement is dependent on the extent of genetic variation present in the germplasm base. Screening for natural genetic variation in drought- and flooding tolerance-related traits, including root system architecture, water and nitrogen-fixation efficiency, and yield performance indices, has helped to identify the best resources for genetic studies in soybean. Genomic resources, including whole-genome sequences of diverse germplasms, millions of single-nucleotide polymorphisms, and high-throughput marker genotyping platforms, have expedited gene and marker discovery for translational genomics in soybean. This review highlights the current knowledge of the genetic diversity and quantitative trait loci associated with root system architecture, canopy wilting, nitrogen-fixation ability, and flooding tolerance that contributes to the understanding of drought- and flooding-tolerance mechanisms in soybean. Next-generation mapping approaches and high-throughput phenotyping will facilitate a better understanding of phenotype-genotype associations and help to formulate genomic-assisted breeding strategies, including genomic selection, in soybean for tolerance to drought and flooding stress.

  12. Genetic diversity and population structure of cottons (Gossypium spp.) of the New World assessed by SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understand its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representin...

  13. Genetic Diversity of Cryptosporidium spp. in Captive Reptiles

    PubMed Central

    Xiao, Lihua; Ryan, Una M.; Graczyk, Thaddeus K.; Limor, Josef; Li, Lixia; Kombert, Mark; Junge, Randy; Sulaiman, Irshad M.; Zhou, Ling; Arrowood, Michael J.; Koudela, Břetislav; Modrý, David; Lal, Altaf A.

    2004-01-01

    The genetic diversity of Cryptosporidium in reptiles was analyzed by PCR-restriction fragment length polymorphism and sequence analysis of the small subunit rRNA gene. A total of 123 samples were analyzed, of which 48 snake samples, 24 lizard samples, and 3 tortoise samples were positive for Cryptosporidium. Nine different types of Cryptosporidium were found, including Cryptosporidium serpentis, Cryptosporidium desert monitor genotype, Cryptosporidium muris, Cryptosporidium parvum bovine and mouse genotypes, one C. serpentis-like parasite in a lizard, two new Cryptosporidium spp. in snakes, and one new Cryptosporidium sp. in tortoises. C. serpentis and the desert monitor genotype were the most common parasites and were found in both snakes and lizards, whereas the C. muris and C. parvum parasites detected were probably the result of ingestion of infected rodents. Sequence and biologic characterizations indicated that the desert monitor genotype was Cryptosporidium saurophilum. Two host-adapted C. serpentis genotypes were found in snakes and lizards. PMID:14766569

  14. Genetic diversity of Cryptosporidium spp. in captive reptiles.

    PubMed

    Xiao, Lihua; Ryan, Una M; Graczyk, Thaddeus K; Limor, Josef; Li, Lixia; Kombert, Mark; Junge, Randy; Sulaiman, Irshad M; Zhou, Ling; Arrowood, Michael J; Koudela, Bretislav; Modrý, David; Lal, Altaf A

    2004-02-01

    The genetic diversity of Cryptosporidium in reptiles was analyzed by PCR-restriction fragment length polymorphism and sequence analysis of the small subunit rRNA gene. A total of 123 samples were analyzed, of which 48 snake samples, 24 lizard samples, and 3 tortoise samples were positive for Cryptosporidium: Nine different types of Cryptosporidium were found, including Cryptosporidium serpentis, Cryptosporidium desert monitor genotype, Cryptosporidium muris, Cryptosporidium parvum bovine and mouse genotypes, one C. serpentis-like parasite in a lizard, two new Cryptosporidium spp. in snakes, and one new Cryptosporidium sp. in tortoises. C. serpentis and the desert monitor genotype were the most common parasites and were found in both snakes and lizards, whereas the C. muris and C. parvum parasites detected were probably the result of ingestion of infected rodents. Sequence and biologic characterizations indicated that the desert monitor genotype was Cryptosporidium saurophilum. Two host-adapted C. serpentis genotypes were found in snakes and lizards.

  15. Genetic diversity of rhizobia nodulating native Vicia spp. in Sweden.

    PubMed

    Ampomah, Osei Yaw; Huss-Danell, Kerstin

    2016-05-01

    Despite the recognition that Rhizobium leguminosarum sv. viciae is the most common symbiont of Vicia species worldwide, there is no available information on rhizobia nodulating native Vicia species in Sweden. We have therefore studied the genetic diversity and phylogeny of root nodule bacteria isolated from V. cracca, V. hirsuta, V. sepium, V. tetrasperma and V. sylvatica growing in different locations in Sweden as well as an isolate each from V. cracca in Tromsø, Norway, and V. multicaulis in Siberia, Russia. Out of 25 isolates sampled from the six Vicia species in 12 different locations, there were 14 different genotypes based on the atpD, recA and nodA gene phylogenies. All isolates were classified into Rhizobium leguminosarum sv. viciae group based on the concatenated atpD and recA phylogeny and the nodA phylogeny.

  16. Genetic diversity assessment of summer squash landraces using molecular markers.

    PubMed

    Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

    2013-07-01

    Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash.

  17. EFFECTS OF CHEMICAL CONTAMINANTS ON GENETIC DIVERSITY IN NATURAL POPULATIONS: IMPLICATIONS FOR BIOMONITORING AND ECOTOXICOLOGY

    EPA Science Inventory

    The conservation of genetic diversity has emerged as one of the central issues in conservation biology. Although researchers in the areas of evolutionary biology, population management, and conservation biology routinely investigate genetic variability in natural populations, onl...

  18. HIV-1 Genetic Diversity Among Incident Infections in Mbeya, Tanzania.

    PubMed

    Billings, Erik; Sanders-Buell, Eric; Bose, Meera; Kijak, Gustavo H; Bradfield, Andrea; Crossler, Jacqueline; Arroyo, Miguel A; Maboko, Leonard; Hoffmann, Oliver; Geis, Steffen; Birx, Deborah L; Kim, Jerome H; Michael, Nelson L; Robb, Merlin L; Hoelscher, Michael; Tovanabutra, Sodsai

    2017-04-01

    In preparation for vaccine trials, HIV-1 genetic diversity was surveyed between 2002 and 2006 through the Cohort Development study in the form of a retrospective and prospective observational study in and around the town of Mbeya in Tanzania's Southwest Highlands. This study describes the molecular epidemiology of HIV-1 strains obtained from 97 out of 106 incident HIV-1 infections identified in three subpopulations of participants (one rural, two urban) from the Mbeya area. Near full-genome or half-genome sequencing showed a subtype distribution of 40% C, 17% A1, 1% D, and 42% inter-subtype recombinants. Compared to viral subtyping results previously obtained from the retrospective phase of this study, the overall proportion of incident viral strains did not change greatly during the study course, suggesting maturity of the epidemic. A comparison to a current Phase I-II vaccine being tested in Africa shows ∼17% amino acid sequence difference between the gp120 of the vaccine and subtype C incident strains. Phylogenetic and recombinant breakpoint analysis of the incident strains revealed the emergence of CRF41_CD and many unique recombinants, as well as the presence of six local transmission networks most of which were confined to the rural subpopulation. In the context of vaccine cohort selection, these results suggest distinct infection transmission dynamics within these three geographically close subpopulations. The diversity and genetic sequences of the HIV-1 strains obtained during this study will greatly contribute to the planning, immunogen selection, and analysis of vaccine-induced immune responses observed during HIV-1 vaccine trials in Tanzania and neighboring countries.

  19. [Genetic Diversity of Vitis vinifera L. in Azerbaijan].

    PubMed

    Salayeva, S J; Ojaghi, J M; Pashayeva, A N; Izzatullayeva, V I; Akhundova, E M; Akperov, Z I

    2016-04-01

    To examine the genetic diversity of Vitis vinifera L., growing in the Republic of Azerbaijan in the region near the Caspian Sea, nuclear genomes of 31 cultivated and 34 wild grapevine accessions were studied at population and individual levels using five ISSR primers. In total, 51 fragments were amplified, of which 45 were found to be polymorphic. A high level of polymorphism was revealed (the mean PPF and PIC values constituted 87.69% and 0.94, respectively). High values of the EMR, MI, and RP indices showed the effectiveness of the application of ISSR primers and the possibility of their use in further investigations in this direction. Cluster analysis based on Nei's genetic distance values showed that all genotypes could be grouped into seven main clusters. Furthermore, no differences between the wild and cultivated grape wine accessions were revealed. For instance, there was no distinct distribution of the accessions according to their geographical localization. On the basis of the PIC values, the group of cultivars from Absheron Peninsula--was distinguished by the highest polymorphism level (PIC = 0.36). Natural populations from the Guba and Shabran regions were characterized by a relatively low polymorphism level (PIC = 0.31 and PIC = 0.28, respectively); and a wild population from Nabran demonstrated the lowest polymorphism level (PIC = 0.25). The data obtained confirmed paleontological and historical data of different periods, provide the supposition that Azerbaijan is the center of diversity of V. vinifera L. In addition, our data indicate that Azerbaijan grape landraces originated from local wild forms.

  20. Genetic Diversity of Echinococcus granulosus in Center of Iran

    PubMed Central

    Pestechian, Nader; Tajedini, Mohammadhasan; Rostami-Nejad, Mohammad; Mousavi, Mohammad; Yousofi, Hosseinali; Haghjooy Javanmard, Shaghayegh

    2014-01-01

    Hydatid cyst caused by Echinococcus granulosus is one of the most important parasitic diseases around the world and many countries in Asia, including Iran, are involved with this infection. This disease can cause high mortality in humans as well as economic losses in livestock. To date, several molecular methods have been used to determine the genetic diversity of E. granulosus. So far, identification of E. granulosus using real-time PCR fluorescence-based quantitative assays has not been studied worldwide, also in Iran. Therefore, the aim of this study was to investigate the genetic diversity of E. granulosus from center of Iran using real-time PCR method. A total of 71 hydatid cysts were collected from infected sheep, goat, and cattle slaughtered in Isfahan, Iran during 2013. DNA was extracted from protoscolices and/or germinal layers from each individual cyst and used as template to amplify the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) (420 bp). Five cattle isolates out of 71 isolates were sterile and excluded from further investigation. Overall, of 66 isolates, partial sequences of the cox1 gene of E. granulosus indicated the presence of genotypes G1 in 49 isolates (74.2%), G3 in 15 isolates (22.7%), and G6 in 2 isolates (3.0%) in infected intermediate hosts. Sixteen sequences of G1 genotype had microgenetic variants, and they were compared to the original sequence of cox1. However, isolates identified as G3 and G6 genotypes were completely consistent with original sequences. G1 genotype in livestock was the dominant genotype in Isfahan region, Iran. PMID:25246720

  1. Epidemiology and genetic diversity of Taenia asiatica: a systematic review

    PubMed Central

    2014-01-01

    Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species. PMID:24450957

  2. High local genetic diversity of canine parvovirus from Ecuador.

    PubMed

    Aldaz, Jaime; García-Díaz, Juan; Calleros, Lucía; Sosa, Katia; Iraola, Gregorio; Marandino, Ana; Hernández, Martín; Panzera, Yanina; Pérez, Ruben

    2013-09-27

    Canine parvovirus (CPV) comprises three antigenic variants (2a, 2b, and 2c) that are distributed globally with different frequencies and levels of genetic variability. CPVs from central Ecuador were herein analyzed to characterize the strains and to provide new insights into local viral diversity, evolution, and pathogenicity. Variant prevalence was analyzed by PCR and partial sequencing for 53 CPV-positive samples collected during 2011 and 2012. The full-length VP2 gene was sequenced in 24 selected strains and a maximum-likelihood phylogenetic tree was constructed using both Ecuadorian and worldwide strains. Ecuadorian CPVs have a remarkable genetic diversity that includes the circulation of all three variants and the existence of different evolutionary groups or lineages. CPV-2c was the most prevalent variant (54.7%), confirming the spread of this variant in America. Ecuadorian CPV-2c strains clustered in two lineages, which represent the first evidence of polyphyletic CPV-2c circulating in South America. CPV-2a strains constituted 41.5% of the samples and clustered in a single lineage. The two detected CPV-2b strains (3.8%) were clearly polyphyletic and appeared related to Ecuadorian CPV-2a or foreign CPV-2b strains. Besides the substitution at residue 426 that is used to identify the variants, two amino acid changes occurred in Ecuadorian strains: Val139Iso and Thr440Ser. Ser(440) occurred in a biologically relevant domain of VP2 and is here described for the first time in CPV. The associations of Ecuadorian CPV-2c and CPV-2a with clinical symptoms indicate that dull mentation, hemorrhagic gastroenteritis and hypothermia occurred more frequently in infection with CPV-2c than with CPV-2a.

  3. Epidemiology and genetic diversity of Taenia asiatica: a systematic review.

    PubMed

    Ale, Anita; Victor, Bjorn; Praet, Nicolas; Gabriël, Sarah; Speybroeck, Niko; Dorny, Pierre; Devleesschauwer, Brecht

    2014-01-22

    Taenia asiatica has made a remarkable journey through the scientific literature of the past 50 years, starting with the paradoxical observation of high prevalences of T. saginata-like tapeworms in non-beef consuming populations, to the full description of its mitochondrial genome. Experimental studies conducted in the 1980s and 1990s have made it clear that the life cycle of T. asiatica is comparable to that of T. saginata, except for pigs being the preferential intermediate host and liver the preferential location of the cysts. Whether or not T. asiatica can cause human cysticercosis, as is the case for Taenia solium, remains unclear. Given the specific conditions needed to complete its life cycle, in particular the consumption of raw or poorly cooked pig liver, the transmission of T. asiatica shows an important ethno-geographical association. So far, T. asiatica has been identified in Taiwan, South Korea, Indonesia, the Philippines, Thailand, south-central China, Vietnam, Japan and Nepal. Especially this last observation indicates that its distribution is not restricted to South-East-Asia, as was thought so far. Indeed, the molecular tools developed over the last 20 years have made it increasingly possible to differentiate T. asiatica from other taeniids. Such tools also indicated that T. asiatica is related more closely to T. saginata than to T. solium, feeding the debate on its taxonomic status as a separate species versus a subspecies of T. saginata. Furthermore, the genetic diversity within T. asiatica appears to be very minimal, indicating that this parasite may be on the verge of extinction. However, recent studies have identified potential hybrids between T. asiatica and T. saginata, reopening the debate on the genetic diversity of T. asiatica and its status as a separate species.

  4. Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network.

    PubMed

    Jangjoo, Maryam; Matter, Stephen F; Roland, Jens; Keyghobadi, Nusha

    2016-09-27

    Demographic bottlenecks that occur when populations fluctuate in size erode genetic diversity, but that diversity can be recovered through immigration. Connectivity among populations and habitat patches in the landscape enhances immigration and should in turn facilitate recovery of genetic diversity after a sudden reduction in population size. For the conservation of genetic diversity, it may therefore be particularly important to maintain connectivity in the face of factors that increase demographic instability, such as climate change. However, a direct link between connectivity and recovery of genetic diversity after a demographic bottleneck has not been clearly demonstrated in an empirical system. Here, we show that connectivity of habitat patches in the landscape contributes to the maintenance of genetic diversity after a demographic bottleneck. We were able to monitor genetic diversity in a network of populations of the alpine butterfly, Parnassius smintheus, before, during, and after a severe reduction in population size that lasted two generations. We found that allelic diversity in the network declined after the demographic bottleneck but that less allelic diversity was lost from populations occupying habitat patches with higher connectivity. Furthermore, the effect of connectivity on allelic diversity was important during the demographic recovery phase. Our results demonstrate directly the ability of connectivity to mediate the rescue of genetic diversity in a natural system.

  5. Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network

    PubMed Central

    Jangjoo, Maryam; Matter, Stephen F.; Roland, Jens; Keyghobadi, Nusha

    2016-01-01

    Demographic bottlenecks that occur when populations fluctuate in size erode genetic diversity, but that diversity can be recovered through immigration. Connectivity among populations and habitat patches in the landscape enhances immigration and should in turn facilitate recovery of genetic diversity after a sudden reduction in population size. For the conservation of genetic diversity, it may therefore be particularly important to maintain connectivity in the face of factors that increase demographic instability, such as climate change. However, a direct link between connectivity and recovery of genetic diversity after a demographic bottleneck has not been clearly demonstrated in an empirical system. Here, we show that connectivity of habitat patches in the landscape contributes to the maintenance of genetic diversity after a demographic bottleneck. We were able to monitor genetic diversity in a network of populations of the alpine butterfly, Parnassius smintheus, before, during, and after a severe reduction in population size that lasted two generations. We found that allelic diversity in the network declined after the demographic bottleneck but that less allelic diversity was lost from populations occupying habitat patches with higher connectivity. Furthermore, the effect of connectivity on allelic diversity was important during the demographic recovery phase. Our results demonstrate directly the ability of connectivity to mediate the rescue of genetic diversity in a natural system. PMID:27621433

  6. Diversity and Moral Reasoning: How Negative Diverse Peer Interactions Affect the Development of Moral Reasoning in Undergraduate Students

    ERIC Educational Resources Information Center

    Mayhew, Matthew J.; Engberg, Mark E.

    2010-01-01

    How do interactions with diverse peers affect moral reasoning development? Results from a longitudinal study of 171 students enrolled in an Intergroup Dialogue or Introduction to Sociology course indicate that students who experience more negative interactions with diverse peers report lower developmental gains in moral reasoning, although the…

  7. Genetic diversity of microsatellite loci in hierarchically structured populations.

    PubMed

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  8. Genetic signatures of ecological diversity along an urbanization gradient

    PubMed Central

    O’Donnell, James L.; Lowell, Natalie C.; Shelton, Andrew O.; Samhouri, Jameal F.; Hennessey, Shannon M.; Feist, Blake E.; Williams, Gregory D.

    2016-01-01

    Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community. PMID:27672503

  9. Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae).

    PubMed

    Yamada, Shuntaro; Ohkubo, Satoshi; Miyashita, Hideaki; Setoguchi, Hiroaki

    2012-09-01

    The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats.

  10. Optimal Sequencing Strategies for Surveying Molecular Genetic Diversity

    PubMed Central

    Pluzhnikov, A.; Donnelly, P.

    1996-01-01

    Two commonly used measures of genetic diversity for intraspecies DNA sequence data are based, respectively, on the number of segregating sites, and on the average number of pairwise nucleotide differences. Expressions are derived for their variance in the presence of intragenic recombination for a panmictic population of fixed size that is at neutral equilibrium at the region sequenced. We show that, in contrast to the slow decrease in variance with increasing sample size, if the recombination rate is nonzero, the asymptotic rate of decrease of variance with increasing sequence length, for fixed sample size, is quite rapid. In particular, it is close to that which would be obtained by sequencing independent chromosome regions. The correlation between measures of diversity from linked regions is also examined. For a given total number of bases sequenced in a particular region, optimal sequencing strategies are derived. These typically involve sequencing relatively few (three to 10) long copies of the region. Under optimal strategies, the variances of the two measures are very similar for most parameter values considered. Results concerning optimal sequencing strategies will be sensitive to gross departures from the underlying assumptions, such as population bottlenecks, selective sweeps, and substantial population substructure. PMID:8913765

  11. Genetic diversity, structure and differentiation in cultivated walnut (juglans regia l.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of w...

  12. The Genetic Diversity of Mesodinium and Associated Cryptophytes

    PubMed Central

    Johnson, Matthew D.; Beaudoin, David J.; Laza-Martinez, Aitor; Dyhrman, Sonya T.; Fensin, Elizabeth; Lin, Senjie; Merculief, Aaron; Nagai, Satoshi; Pompeu, Mayza; Setälä, Outi; Stoecker, Diane K.

    2016-01-01

    Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions. PMID:28066344

  13. The Genetic Diversity of Mesodinium and Associated Cryptophytes.

    PubMed

    Johnson, Matthew D; Beaudoin, David J; Laza-Martinez, Aitor; Dyhrman, Sonya T; Fensin, Elizabeth; Lin, Senjie; Merculief, Aaron; Nagai, Satoshi; Pompeu, Mayza; Setälä, Outi; Stoecker, Diane K

    2016-01-01

    Ciliates from the genus Mesodinium are globally distributed in marine and freshwater ecosystems and may possess either heterotrophic or mixotrophic nutritional modes. Members of the Mesodinium major/rubrum species complex photosynthesize by sequestering and maintaining organelles from cryptophyte prey, and under certain conditions form periodic or recurrent blooms (= red tides). Here, we present an analysis of the genetic diversity of Mesodinium and cryptophyte populations from 10 environmental samples (eight globally dispersed habitats including five Mesodinium blooms), using group-specific primers for Mesodinium partial 18S, ITS, and partial 28S rRNA genes as well as cryptophyte large subunit RuBisCO genes (rbcL). In addition, 22 new cryptophyte and four new M. rubrum cultures were used to extract DNA and sequence rbcL and 18S-ITS-28S genes, respectively, in order to provide a stronger phylogenetic context for our environmental sequences. Bloom samples were analyzed from coastal Brazil, Chile, two Northeastern locations in the United States, and the Pribilof Islands within the Bering Sea. Additionally, samples were also analyzed from the Baltic and Barents Seas and coastal California under non-bloom conditions. Most blooms were dominated by a single Mesodinium genotype, with coastal Brazil and Chile blooms composed of M. major and the Eastern USA blooms dominated by M. rubrum variant B. Sequences from all four blooms were dominated by Teleaulax amphioxeia-like cryptophytes. Non-bloom communities revealed more diverse assemblages of Mesodinium spp., including heterotrophic species and the mixotrophic Mesodinium chamaeleon. Similarly, cryptophyte diversity was also higher in non-bloom samples. Our results confirm that Mesodinium blooms may be caused by M. major, as well as multiple variants of M. rubrum, and further implicate T. amphioxeia as the key cryptophyte species linked to these phenomena in temperate and subtropical regions.

  14. Genetic diversity among sea otter isolates of Toxoplasma gondii

    USGS Publications Warehouse

    Sundar, N.; Cole, R.A.; Thomas, N.J.; Majumdar, D.; Dubey, J.P.; Su, C.

    2008-01-01

    Sea otters (Enhydra lutris) have been reported to become infected with Toxoplasma gondii and at times succumb to clinical disease. Here, we determined genotypes of 39 T. gondii isolates from 37 sea otters in two geographically distant locations (25 from California and 12 from Washington). Six genotypes were identified using 10 PCR-RFLP genetic markers including SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico, and by DNA sequencing of loci SAG1 and GRA6 in 13 isolates. Of these 39 isolates, 13 (33%) were clonal Type II which can be further divided into two groups at the locus Apico. Two of the 39 isolates had Type II alleles at all loci except a Type I allele at locus L358. One isolate had Type II alleles at all loci except the Type I alleles at loci L358 and Apico. One isolate had Type III alleles at all loci except Type II alleles at SAG2 and Apico. Two sea otter isolates had a mixed infection. Twenty-one (54%) isolates had an unique allele at SAG1 locus. Further genotyping or DNA sequence analysis for 18 of these 21 isolates at loci SAG1 and GRA6 revealed that there were two different genotypes, including the previously identified Type X (four isolates) and a new genotype named Type A (14 isolates). The results from this study suggest that the sea otter isolates are genetically diverse.

  15. Internal lattice reconfiguration for diversity tuning in Cellular Genetic Algorithms.

    PubMed

    Morales-Reyes, Alicia; Erdogan, Ahmet T

    2012-01-01

    Cellular Genetic Algorithms (cGAs) have attracted the attention of researchers due to their high performance, ease of implementation and massive parallelism. Maintaining an adequate balance between exploitative and explorative search is essential when studying evolutionary optimization techniques. In this respect, cGAs inherently possess a number of structural configuration parameters that are able to sustain diversity during evolution. In this study, the internal reconfiguration of the lattice is proposed to constantly or adaptively control the exploration-exploitation trade-off. Genetic operators are characterized in their simplest form since algorithmic performance is assessed on implemented reconfiguration mechanisms. Moreover, internal reconfiguration allows the adjacency of individuals to be maintained. Hence, any improvement in performance is only a consequence of topological changes. Two local selection methods presenting opposite selection pressures are used in order to evaluate the influence of the proposed techniques. Problems ranging from continuous to real world and combinatorial are tackled. Empirical results are supported statistically in terms of efficiency and efficacy.

  16. Genetic diversity of Leishmania infantum field populations from Brazil.

    PubMed

    Segatto, Marcela; Ribeiro, Lucas Secchim; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery; Oliveira, Márcia Rosa de; Carvalho, Sílvio Fernando Guimarães; Macedo, Andréa Mara; Valadares, Helder Magno Silva; Dietze, Reynaldo; Brito, Cristiana Ferreira Alves de; Lemos, Elenice Moreira

    2012-02-01

    Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin.

  17. Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.

    PubMed

    Dubey, J P; Choudhary, S; Tilahun, G; Tiao, N; Gebreyes, W A; Zou, X; Su, C

    2013-09-01

    Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia.

  18. Population structure and genetic diversity of moose in Alaska.

    PubMed

    Schmidt, Jennifer I; Hundertmark, Kris J; Bowyer, R Terry; McCracken, Kevin G

    2009-01-01

    Moose (Alces alces) are highly mobile mammals that occur across arboreal regions of North America, Europe, and Asia. Alaskan moose (Alces alces gigas) range across much of Alaska and are primary herbivore consumers, exerting a prominent influence on ecosystem structure and functioning. Increased knowledge gained from population genetics provides insights into their population dynamics, history, and dispersal of these unique large herbivores and can aid in conservation efforts. We examined the genetic diversity and population structure of moose (n = 141) with 8 polymorphic microsatellites from 6 regions spanning much of Alaska. Expected heterozygosity was moderate (H(E) = 0.483-0.612), and private alleles ranged from 0 to 6. Both F(ST) and R(ST) indicated significant population structure (P < 0.001) with F(ST) < 0.109 and R(ST) < 0.125. Results of analyses from STRUCTURE indicated 2 prominent population groups, a mix of moose from the Yakutat and Tetlin regions versus all other moose, with slight substructure observed among the second population. Estimates of dispersal differed between analytical approaches, indicating a high level of historical or current gene flow. Mantel tests indicated that isolation-by-distance partially explained observed structure among moose populations (R(2) = 0.45, P < 0.01). Finally, there was no evidence of bottlenecks either at the population level or overall. We conclude that weak population structure occurs among moose in Alaska with population expansion from interior Alaska westward toward the coast.

  19. Adapting populations in space: clonal interference and genetic diversity

    NASA Astrophysics Data System (ADS)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  20. Effects of grazer presence on genetic structure of a phenotypically diverse diatom population.

    PubMed

    Sjöqvist, C; Kremp, A; Lindehoff, E; Båmstedt, U; Egardt, J; Gross, S; Jönsson, M; Larsson, H; Pohnert, G; Richter, H; Selander, E; Godhe, A

    2014-01-01

    Studies of predator-prey systems in both aquatic and terrestrial environments have shown that grazers structure the intraspecific diversity of prey species, given that the prey populations are phenotypically variable. Populations of phytoplankton have traditionally considered comprising only low intraspecific variation, hence selective grazing as a potentially structuring factor of both genetic and phenotypic diversity has not been comprehensively studied. In this study, we compared strain specific growth rates, production of polyunsaturated aldehydes, and chain length of the marine diatom Skeletonema marinoi in both grazer and non-grazer conditions by conducting monoclonal experiments. Additionally, a mesocosm experiment was performed with multiclonal experimental S. marinoi populations exposed to grazers at different levels of copepod concentration to test effects of grazer presence on diatom diversity in close to natural conditions. Our results show that distinct genotypes of a geographically restricted population exhibit variable phenotypic traits relevant to grazing interactions such as chain length and growth rates. Grazer presence affected clonal richness and evenness of multiclonal Skeletonema populations in the mesocosms, likely in conjunction with intrinsic interactions among the diatom strains. Only the production of polyunsaturated aldehydes was not affected by grazer presence. Our findings suggest that grazing can be an important factor structuring diatom population diversity in the sea and emphasize the importance of considering clonal differences when characterizing species and their role in nature.

  1. A nonlinear relationship between genetic diversity and productivity in a polyphagous seed beetle.

    PubMed

    Burls, K J; Shapiro, J; Forister, M L; Hoelzer, G A

    2014-05-01

    There has been a renewed interest in the effects of genetic diversity on population-level and community-level processes. Many of these studies have found non-additive, positive effects of diversity, but these studies have rarely examined ecological mechanisms by which diverse populations increase productivity. We used the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) to study genetic diversity in insect host preference and fecundity and its effects on total productivity and resource use. We created genetically distinct lineages that varied in host preference and fecundity and then assembled groups consisting of one, three, five, or all ten lineages. We found that lineages with intermediate diversity had the highest productivity, though resource use did not change in diverse groups. In addition, lineages showed substantial plasticity in host preference when preference was assayed either individually or in groups, and productivity was much lower in groups than predicted by individual assays. These results highlight the interplay of genetic diversity, resource variation, and phenotypic plasticity in determining the ecological consequences of genetic diversity. In addition, when plasticity modifies a population's response to population density, this may create a complex interaction between genetic diversity and density, influencing selective pressures on the population and potentially maintaining genetic diversity across generations.

  2. Low genetic diversity and strong but shallow population differentiation suggests genetic homogenization by metapopulation dynamics in a social spider.

    PubMed

    Settepani, V; Bechsgaard, J; Bilde, T

    2014-12-01

    Mating systems and population dynamics influence genetic diversity and structure. Species that experience inbreeding and limited gene flow are expected to evolve isolated, divergent genetic lineages. Metapopulation dynamics with frequent extinctions and colonizations may, on the other hand, deplete and homogenize genetic variation, if extinction rate is sufficiently high compared to the effect of drift in local demes. We investigated these theoretical predictions empirically in social spiders that are highly inbred. Social spiders show intranest mating, female-biased sex ratio, and frequent extinction and colonization events, factors that deplete genetic diversity within nests and populations and limit gene flow. We characterized population genetic structure in Stegodyphus sarasinorum, a social spider distributed across the Indian subcontinent. Species-wide genetic diversity was estimated over approximately 2800 km from Sri Lanka to Himalayas, by sequencing 16 protein-coding nuclear loci. We found 13 SNPs in 6592 bp (π = 0.00045) indicating low species-wide nucleotide diversity. Three genetic lineages were strongly differentiated; however, only one fixed difference among them suggests recent divergence. This is consistent with a scenario of metapopulation dynamics that homogenizes genetic diversity across the species' range. Ultimately, low standing genetic variation may hamper a species' ability to track environmental change and render social inbreeding spiders 'evolutionary dead-ends'.

  3. Patterns of genetic diversity in the polymorphic ground snake (Sonora semiannulata).

    PubMed

    Cox, Christian L; Chippindale, Paul T

    2014-08-01

    We evaluated the genetic diversity of a snake species with color polymorphism to understand the evolutionary processes that drive genetic structure across a large geographic region. Specifically, we analyzed genetic structure of the highly polymorphic ground snake, Sonora semiannulata, (1) among populations, (2) among color morphs (3) at regional and local spatial scales, using an amplified fragment length polymorphism dataset and multiple population genetic analyses, including FST-based and clustering analytical techniques. Based upon these methods, we found that there was moderate to low genetic structure among populations. However, this diversity was not associated with geographic locality at either spatial scale. Similarly, we found no evidence for genetic divergence among color morphs at either spatial scale. These results suggest that despite dramatic color polymorphism, this phenotypic diversity is not a major driver of genetic diversity within or among populations of ground snakes. We suggest that there are two mechanisms that could explain existing genetic diversity in ground snakes: recent range expansion from a genetically diverse founder population and current or recent gene flow among populations. Our findings have further implications for the types of color polymorphism that may generate genetic diversity in snakes.

  4. Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations.

    PubMed

    Zhang, Junxia; Jiao, Ting; Zhao, Shengguo

    2016-05-13

    Increased global use of highly productive commercial breeds has reduced genetic diversity in indigenous breeds. It is necessary to protect local porcine breeds. We therefore assessed the level of genetic diversity in global swine populations. In this study, the mitochondrial DNA D-loop region was examined in 1010 sequences from indigenous pigs and commercial swine as well as 3424 publicly available sequences We identified 334 haplotypes and 136 polymorphic sites. Genetic diversity was analyzed based on basic parameters, including haplotype diversity, nucleotide diversity and the average number of nucleotide differences, and also assessed by principal component analysis. A comparison of nucleotide diversity and the average number of nucleotide differences between indigenous breeds and commercial breeds showed that indigenous pigs had a lower level of diversity than commercial breeds. The principle component analysis result also showed the genetic diversity of the indigenous breeds was lower than that of commercial breeds. Collectively, our results reveal the Southeast Asian porcine population exhibited the higher nucleotide diversity, whereas Chinese population appeared consistently lower level in Asia. European, American and Oceanian pigs had a relatively higher degree of genetic diversity compared with that of Asian pigs. In conclusion, our findings indicated that the introgression of commercial into indigenous breeds decreased indigenous breeds' genetic diversity.

  5. Concordance between genetic and species diversity in coral reef fishes across the Pacific Ocean biodiversity gradient.

    PubMed

    Messmer, Vanessa; Jones, Geoffrey P; Munday, Philip L; Planes, Serge

    2012-12-01

    The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ∼1600 species; New Caledonia: ∼1400 species; French Polynesia: ∼800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential.

  6. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    PubMed Central

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

  7. Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits.

    PubMed

    Moreno-Estrada, Andrés; Gignoux, Christopher R; Fernández-López, Juan Carlos; Zakharia, Fouad; Sikora, Martin; Contreras, Alejandra V; Acuña-Alonzo, Victor; Sandoval, Karla; Eng, Celeste; Romero-Hidalgo, Sandra; Ortiz-Tello, Patricia; Robles, Victoria; Kenny, Eimear E; Nuño-Arana, Ismael; Barquera-Lozano, Rodrigo; Macín-Pérez, Gastón; Granados-Arriola, Julio; Huntsman, Scott; Galanter, Joshua M; Via, Marc; Ford, Jean G; Chapela, Rocío; Rodriguez-Cintron, William; Rodríguez-Santana, Jose R; Romieu, Isabelle; Sienra-Monge, Juan José; del Rio Navarro, Blanca; London, Stephanie J; Ruiz-Linares, Andrés; Garcia-Herrera, Rodrigo; Estrada, Karol; Hidalgo-Miranda, Alfredo; Jimenez-Sanchez, Gerardo; Carnevale, Alessandra; Soberón, Xavier; Canizales-Quinteros, Samuel; Rangel-Villalobos, Héctor; Silva-Zolezzi, Irma; Burchard, Esteban Gonzalez; Bustamante, Carlos D

    2014-06-13

    Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

  8. Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers

    PubMed Central

    Sun, Rongxi; Lin, Furong; Huang, Ping; Zheng, Yongqi

    2016-01-01

    Chinese sweetgum (Liquidambar formosana) is a relatively fast-growing ecological pioneer species. It is widely used for multiple purposes. To assess the genetic diversity and genetic differentiation of the species, genic SSR markers were mined from transcriptome data for subsequent analysis of the genetic diversity and population structure of natural populations. A total of 10645 potential genic SSR loci were identified in 80482 unigenes. The average frequency was one SSR per 5.12 kb, and the dinucleotide unit was the most abundant motif. A total of 67 alleles were found, with a mean of 6.091 alleles per locus and a mean polymorphism information content of 0.390. Moreover, the species exhibited a relatively moderate level of genetic diversity (He = 0.399), with the highest was found in population XY (He = 0.469). At the regional level, the southwestern region displayed the highest genetic diversity (He = 0.435) and the largest number of private alleles (n = 5), which indicated that the Southwestern region may be the diversity hot spot of L. formosana. The AMOVA results showed that variation within populations (94.02%) was significantly higher than among populations (5.98%), which was in agreement with the coefficient of genetic differentiation (Fst = 0.076). According to the UPGMA analysis and principal coordinate analysis and confirmed by the assignment test, 25 populations could be divided into three groups, and there were different degrees of introgression among populations. No correlation was found between genetic distance and geographic distance (P > 0.05). These results provided further evidence that geographic isolation was not the primary factor leading to the moderate genetic differentiation of L. formosana. As most of the genetic diversity of L. formosana exists among individuals within a population, individual plant selection would be an effective way to use natural variation in genetic improvement programs. This would be helpful to not only protect the

  9. Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits.

    PubMed

    Achleitner, Andreas; Tinker, Nicholas A; Zechner, Elisabeth; Buerstmayr, Hermann

    2008-11-01

    One hundred and fourteen oat (Avena sativa L.) varieties of worldwide origin were evaluated for genetic diversity based on 77 molecular polymorphisms produced by eight selective AFLP primer combinations. Genetic similarity, calculated using the DICE coefficient, was used for cluster analysis and principal component analysis was applied. In addition population structure was explored to identify discrete subpopulations based on allele frequency. Although clustering and population structure showed relationships with region and country of origin, there was no obvious relationship to hull presence or hull colour. Oat varieties originating from European breeding programs showed less diversity than varieties originating from North and South America. Associations between AFLP markers and agronomic traits (grain yield, groat yield, panicle emergence, plant height, and lodging) as well as kernel quality traits (kernel weight, test weight, screening percent and groat percent) were also investigated. Marker-trait associations were tested using a naïve simple regression model and five additional models that account for population structure. Significant associations were found for 23 AFLP markers, with many of these affecting multiple traits. This study demonstrates that diversity can be significantly enhanced using a global collection, and provides evidence for marker-trait associations that can be validated in segregating populations and exploited through marker-assisted selection.

  10. Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations.

    PubMed

    Magalhães, Vanessa; Abrantes, Joana; Munõz-Pajares, Antonio Jesús; Esteves, Pedro J

    2015-10-01

    The European rabbit (Oryctolagus cuniculus) natural populations within the species native region, the Iberian Peninsula, are considered a reservoir of genetic diversity. Indeed, the Iberia was a Pleistocene refuge to the species and currently two subspecies are found in the peninsula (Oryctolagus cuniculus cuniculus and Oryctolagus cuniculus algirus). The genes of the major histocompatibility complex (MHC) have been substantially studied in wild populations due to their exceptional variability, believed to be pathogen driven. They play an important function as part of the adaptive immune system affecting the individual fitness and population viability. In this study, the MHC variability was assessed by analysing the exon 2 of the DQA gene in several European rabbit populations from Portugal, Spain and France and in domestic breeds. Twenty-eight DQA alleles were detected, among which 18 are described for the first time. The Iberian rabbit populations are well differentiated from the French population and domestic breeds. The Iberian populations retained the higher allelic diversity with the domestic breeds harbouring the lowest; in contrast, the DQA nucleotide diversity was higher in the French population. Signatures of positive selection were detected in four codons which are putative peptide-binding sites and have been previously detected in other mammals. The evolutionary relationships showed instances of trans-species polymorphism. Overall, our results suggest that the DQA in European rabbits is evolving under selection and genetic drift.

  11. Genetic diversity of Arcobacter isolated from bivalves of Adriatic and their interactions with Mytilus galloprovincialis hemocytes.

    PubMed

    Ottaviani, Donatella; Mosca, Francesco; Chierichetti, Serena; Tiscar, Pietro Giorgio; Leoni, Francesca

    2017-02-01

    The human food-borne pathogens Arcobacter butzleri and A. cryaerophilus have been frequently isolated from the intestinal tracts and fecal samples of different farm animals and, after excretion, these microorganisms can contaminate the environment, including the aquatic one. In this regard, A. butzleri and A. cryaerophilus have been detected in seawater and bivalves of coastal areas which are affected by fecal contamination. The capability of bivalve hemocytes to interact with bacteria has been proposed as the main factor inversely conditioning their persistence in the bivalve. In this study, 12 strains of Arcobacter spp. were isolated between January and May 2013 from bivalves of Central Adriatic Sea of Italy in order to examine their genetic diversity as well as in vitro interactions with bivalve components of the immune response, such as hemocytes. Of these, seven isolates were A. butzleri and five A. cryaerophilus, and were genetically different. All strains showed ability to induce spreading and respiratory burst of Mytilus galloprovincialis hemocytes. Overall, our data demonstrate the high genetic diversity of these microorganisms circulating in the marine study area. Moreover, the Arcobacter-bivalve interaction suggests that they do not have a potential to persist in the tissues of M. galloprovincialis.

  12. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout.

    PubMed

    Kovach, Ryan P; Muhlfeld, Clint C; Wade, Alisa A; Hand, Brian K; Whited, Diane C; DeHaan, Patrick W; Al-Chokhachy, Robert; Luikart, Gordon

    2015-02-06

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4-7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = -0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already

  13. Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

    USGS Publications Warehouse

    Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

    2015-01-01

    Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already

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

    PubMed

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

    2016-01-01

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

  15. Genetic Structure and Diversity among U.S. sheep breeds: Identification of the major gene pools.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding existing levels of genetic diversity of sheep breeds facilitates in situ and ex situ conservation activities. A comprehensive evaluation of US sheep breeds has not been previously performed therefore we evaluated the genetic diversity among and within 28 US sheep breeds. Both major and...

  16. Elm genetic diversity and hybridization in the presence of Dutch elm disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dutch elm disease (DED) has devastated native North American elm species for more than 75 years. The impact of DED on the genetic diversity of one native elm species, U. rubra or slippery elm, is summarized and its potential impact on the genetic diversity of the other four North American native elm...

  17. Cryptosporidium within-host genetic diversity: systematic bibliographical search and narrative overview.

    PubMed

    Grinberg, Alex; Widmer, Giovanni

    2016-07-01

    Knowledge of the within-host genetic diversity of a pathogen often has broad implications for disease management. Cryptosporidium protozoan parasites are among the most common causative agents of infectious diarrhoea. Current limitations of in vitro culture impose the use of uncultured isolates obtained directly from the hosts as operational units of Cryptosporidium genotyping. The validity of this practice is centred on the assumption of genetic homogeneity of the parasite within the host, and genetic studies often take little account of the within-host genetic diversity of Cryptosporidium. Yet, theory and experimental evidence contemplate genetic diversity of Cryptosporidium at the within-host scale, but this diversity is not easily identified by genotyping methods ill-suited for the resolution of DNA mixtures. We performed a systematic bibliographical search of the occurrence of within-host genetic diversity of Cryptosporidium parasites in epidemiological samples, between 2005 and 2015. Our results indicate that genetic diversity at the within-host scale, in the form of mixed species or intra-species diversity, has been identified in a large number (n=55) of epidemiological surveys of cryptosporidiosis in variable proportions, but has often been treated as a secondary finding and not analysed. As in malaria, there are indications that the scale of this diversity varies between geographical regions, perhaps depending on the prevailing transmission pathways. These results provide a significant knowledge base from which to draw alternative population genetic structure models, some of which are discussed in this paper.

  18. Genetic Diversity in a Collection of Chinese Sorghum Landraces Assessed by Microsattelites

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity was characterized in a collection of 171 sorghum landraces originally gathered from the colder region (primarily the northwestern provinces) of China. Genetic diversity was analyzed using 41 microsattelite or simple sequence repeat (SSR) markers distributed throughout the 10 chromo...

  19. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide molecular markers are readily being applied to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorp...

  20. Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains

    SciTech Connect

    Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

    2006-07-06

    Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.

  1. Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere

    PubMed Central

    Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai

    2009-01-01

    The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging to six bacterial divisions, namely β-, γ-, α-Proteobacteria, Sphingobacteria, Bacilli, and Actinobacteria. Especially, γ-Proteobacteria consisting of Pseudomonas, Enterobacter, Serratia, Pantoea, Erwinia and Stenotrophomonas genus encountered 18 different ARDRA groups. Results also showed a greater siderophore-producing bacterial diversity than previous researches. For example, Sphingobacterium (isolates G-2-21-1 and G-2-27-2), Pseudomonas poae (isolate G-2-1-1), Enterobacter endosymbiont (isolates G-2-10-2 and N-5-10), Delftia acidovorans (isolate G-1-15), and Achromobacter xylosoxidans (isolates N-46-11HH and N-5-20) were reported to be able to produce siderophores under low-iron conditions for the first time. Gram-negative isolates were more frequently encountered, with more than 95% total frequency. For Gram-positive bacteria, the Bacillus and Rhodococcus were the only two genera, with 1.7% total frequency. Furthermore, the Pseudomonas and Enterobacter were dominant in this environment, with 44.5% and 24.7% total frequency, respectively. It was also found that 75 percent of the isolates that had the high percentages of siderophore units (% between 40 and 60) belonged to Pseudomonas. Pseudomonas sp. G-229-21 screened out in this study may have potential to apply to low-iron soil to prevent plant soil-borne fungal pathogen diseases. PMID:24031358

  2. Genetic diversity and carriage dynamics of Neisseria lactamica in infants.

    PubMed

    Bennett, Julia S; Griffiths, David T; McCarthy, Noel D; Sleeman, Karen L; Jolley, Keith A; Crook, Derrick W; Maiden, Martin C J

    2005-04-01

    Neisseria lactamica, a harmless human commensal found predominantly in the upper respiratory tracts of infants, is closely related to Neisseria meningitidis, a pathogen of global significance. Colonization with N. lactamica may be responsible for the increase in immunity to meningococcal disease that occurs during childhood, when rates of meningococcal carriage are low. This observation has led to the suggestion that N. lactamica whole cells or components are potential constituents of novel meningococcal vaccines. However, the dynamics of carriage and population diversity of N. lactamica in children are poorly understood, presenting difficulties for the choice of representative isolates for use in vaccine development. This problem was addressed by the multilocus sequence typing of N. lactamica isolates from two longitudinal studies of bacterial carriage in infants. The studies comprised 100 and 216 subjects, with N. lactamica carriage monitored from age 4 weeks until age 96 weeks and from age 2 weeks until age 24 weeks, respectively. The maximum observed carriage rate was 44% at 56 weeks of age, with isolates obtained on multiple visits for the majority (54 of 75, 72%) of carriers. The N. lactamica isolates were genetically diverse, with 69 distinct genotypes recovered from the 75 infants. Carriage was generally long-lived, with an average rate of loss of under 1% per week during the 28 weeks following acquisition. Only 11 of the 75 infants carried more than one genotypically unique isolate during the course of the study. Some participants shared identical isolates with siblings, but none shared identical isolates with their parents. These findings have implications for the design of vaccines based on this organism.

  3. Genetic diversity among Botulinum Neurotoxin-producing clostridial strains.

    PubMed

    Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svensson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

    2007-02-01

    Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism.

  4. Tooth dentin defects reflect genetic disorders affecting bone mineralization

    PubMed Central

    Vital, S. Opsahl; Gaucher, C.; Bardet, C.; Rowe, P.S.; George, A.; Linglart, A.; Chaussain, C.

    2012-01-01

    Several genetic disorders affecting bone mineralization may manifest during dentin mineralization. Dentin and bone are similar in several aspects, especially pertaining to the composition of the extracellular matrix (ECM) which is secreted by well-differentiated odontoblasts and osteoblasts, respectively. However, unlike bone, dentin is not remodelled and is not involved in the regulation of calcium and phosphate metabolism. In contrast to bone, teeth are accessible tissues with the shedding of deciduous teeth and the extractions of premolars and third molars for orthodontic treatment. The feasibility of obtaining dentin makes this a good model to study biomineralization in physiological and pathological conditions. In this review, we focus on two genetic diseases that disrupt both bone and dentin mineralization. Hypophosphatemic rickets is related to abnormal secretory proteins involved in the ECM organization of both bone and dentin, as well as in the calcium and phosphate metabolism. Osteogenesis imperfecta affects proteins involved in the local organization of the ECM. In addition, dentin examination permits evaluation of the effects of the systemic treatment prescribed to hypophosphatemic patients during growth. In conclusion, dentin constitutes a valuable tool for better understanding of the pathological processes affecting biomineralization. PMID:22296718

  5. Grazing Intensity Does Not Affect Plant Diversity in Shortgrass Steppe

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Responses of livestock gain and forage production to grazing intensity in shortgrass steppe are well-established, but effects on basal cover and plant diversity are less so. A long-term grazing intensity study was initiated on shortgrass steppe at the Central Plains Experimental Range (USDA-Agricult...

  6. Genetic Diversity as Consequence of a Microaerobic and Neutrophilic Lifestyle

    PubMed Central

    Krüger, Nora-Johanna; Knüver, Marie-Theres; Zawilak-Pawlik, Anna; Appel, Bernd; Stingl, Kerstin

    2016-01-01

    As a neutrophilic bacterium, Helicobacter pylori is growth deficient under extreme acidic conditions. The gastric pathogen is equipped with an acid survival kit, regulating urease activity by a pH-gated urea channel, opening below pH 6.5. After overcoming acid stress, the bacterium’s multiplication site is situated at the gastric mucosa with near neutral pH. The pathogen exhibits exceptional genetic variability, mainly due to its capability of natural transformation, termed competence. Using single cell analysis, we show here that competence is highly regulated in H. pylori. DNA uptake complex activity was reversibly shut down below pH 6.5. pH values above 6.5 opened a competence window, in which competence development was triggered by the combination of pH increase and oxidative stress. In contrast, addition of sublethal concentrations of the DNA-damaging agents ciprofloxacin or mitomycin C did not trigger competence development under our conditions. An oxygen-sensitive mutant lacking superoxide dismutase (sodB) displayed a higher competent fraction of cells than the wild type under comparable conditions. In addition, the sodB mutant was dependent on adenine for growth in broth and turned into non-cultivable coccoid forms in its absence, indicating that adenine had radical quenching capacity. Quantification of periplasmically located DNA in competent wild type cells revealed outstanding median imported DNA amounts of around 350 kb per cell within 10 min of import, with maximally a chromosomal equivalent (1.6 Mb) in individual cells, far exceeding previous amounts detected in other Gram-negative bacteria. We conclude that the pathogen’s high genetic diversity is a consequence of its enormous DNA uptake capacity, triggered by intrinsic and extrinsic oxidative stress once a neutral pH at the site of chronic host colonization allows competence development. PMID:27166672

  7. Genetic diversity of Phytophthora infestans in the Northern Andean region

    PubMed Central

    2011-01-01

    Background Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, β-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. Results Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. Conclusions The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a. PMID:21303555

  8. Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).

    PubMed

    Nassar, J M; Hamrick, J L; Fleming, T H

    2002-01-01

    We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America.

  9. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques

    PubMed Central

    Onda, Yoshihiko; Mochida, Keiichi

    2016-01-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study. PMID:27499684

  10. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques.

    PubMed

    Onda, Yoshihiko; Mochida, Keiichi

    2016-08-01

    Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.

  11. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation

    PubMed Central

    Turchetto, Caroline; Segatto, Ana Lúcia A.; Mäder, Geraldo; Rodrigues, Daniele M.; Bonatto, Sandro L.; Freitas, Loreta B.

    2016-01-01

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently. PMID:26768602

  12. High levels of genetic diversity and population structure in an endemic and rare species: implications for conservation.

    PubMed

    Turchetto, Caroline; Segatto, Ana Lúcia A; Mäder, Geraldo; Rodrigues, Daniele M; Bonatto, Sandro L; Freitas, Loreta B

    2016-01-13

    The analysis of genetic structure and variability of isolated species is of critical importance in evaluating whether stochastic or human-caused factors are affecting rare species. Low genetic diversity compromises the ability of populations to evolve and reduces their chances of survival under environmental changes. Petunia secreta, a rare and endemic species, is an annual and heliophilous herb that is bee-pollinated and easily recognizable by its purple and salverform corolla. It was described as a new species of the Petunia genus in 2005. Few individuals of P. secreta have been observed in nature and little is known about this species. All the natural populations of P. secreta that were found were studied using 15 microsatellite loci, two intergenic plastid sequences and morphological traits. Statistical analysis was performed to describe the genetic diversity of this rare species and the results compared with those of more widespread and frequent Petunia species from the same geographic area to understand whether factors associated with population size could affect rare species of this genus. The results showed that despite its rarity, P. secreta presented high genetic diversity that was equivalent to or even higher than that of widespread Petunia species. It was shown that this species is divided into two evolutionary lineages, and the genetic differentiation indices between them and other congeneric species presented different patterns. The major risk to P. secreta maintenance is its rarity, suggesting the necessity of a preservation programme and more biological and evolutionary studies that handle the two evolutionary lineages independently.

  13. Genetic diversity of Chlamydia among captive birds from central Argentina.

    PubMed

    Frutos, María C; Monetti, Marina S; Vaulet, Lucia Gallo; Cadario, María E; Fermepin, Marcelo Rodríguez; Ré, Viviana E; Cuffini, Cecilia G

    2015-01-01

    To study the occurrence of Chlamydia spp. and their genetic diversity, we analysed 793 cloacal swabs from 12 avian orders, including 76 genera, obtained from 80 species of asymptomatic wild and captive birds that were examined with conventional nested polymerase chain reaction and quantitative polymerase chain reaction. Chlamydia spp. were not detected in wild birds; however, four species (Chlamydia psittaci, Chlamydia pecorum, Chlamydia pneumoniae and Chlamydia gallinacea) were identified among captive birds (Passeriformes, n = 20; Psittaciformes, n = 15; Rheiformes, n = 8; Falconiformes n = 2; Piciformes n = 2; Anseriformes n = 1; Galliformes n = 1; Strigiformes n = 1). Two pathogens (C. pneumoniae and C. pecorum) were identified simultaneously in samples obtained from captive birds. Based on nucleotide-sequence variations of the ompA gene, three C. psittaci-positive samples detected were grouped into a cluster with the genotype WC derived from mammalian hosts. A single positive sample was phylogenetically related to a new strain of C. gallinacea. This report contributes to our increasing understanding of the abundance of Chlamydia in the animal kingdom.

  14. Genetic diversity of bovine Neospora caninum determined by microsatellite markers.

    PubMed

    Salehi, N; Gottstein, B; Haddadzadeh, H R

    2015-10-01

    Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed.

  15. Dilated cardiomyopathy: the complexity of a diverse genetic architecture.

    PubMed

    Hershberger, Ray E; Hedges, Dale J; Morales, Ana

    2013-09-01

    Remarkable progress has been made in understanding the genetic basis of dilated cardiomyopathy (DCM). Rare variants in >30 genes, some also involved in other cardiomyopathies, muscular dystrophy, or syndromic disease, perturb a diverse set of important myocardial proteins to produce a final DCM phenotype. Large, publicly available datasets have provided the opportunity to evaluate previously identified DCM-causing mutations, and to examine the population frequency of sequence variants similar to those that have been observed to cause DCM. The frequency of these variants, whether associated with dilated or hypertrophic cardiomyopathy, is greater than estimates of disease prevalence. This mismatch might be explained by one or more of the following possibilities: that the penetrance of DCM-causing mutations is lower than previously thought, that some variants are noncausal, that DCM prevalence is higher than previously estimated, or that other more-complex genomics underlie DCM. Reassessment of our assumptions about the complexity of the genomic and phenomic architecture of DCM is warranted. Much about the genomic basis of DCM remains to be investigated, which will require comprehensive genomic studies in much larger cohorts of rigorously phenotyped probands and family members than previously examined.

  16. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

    PubMed Central

    Müller, Romy; Roberts, Charlotte A.; Brown, Terence A.

    2014-01-01

    The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis. PMID:24573854

  17. Genetic Diversity in Gorkhas: an Autosomal STR Study

    PubMed Central

    Preet, Kiran; Malhotra, Seema; Shrivastava, Pankaj; Jain, Toshi; Rawat, Shweta; Varte, L. Robert; Singh, Sayar; Singh, Inderjeet; Sarkar, Soma

    2016-01-01

    Genotyping of highly polymorphic autosomal short tandem repeat (STR) markers is a potent tool for elucidating genetic diversity. In the present study, fifteen autosomal STR markers were analyzed in unrelated healthy male Gorkha individuals (n = 98) serving in the Indian Army by using AmpFlSTR Identifiler Plus PCR Amplification Kit. In total, 138 alleles were observed with corresponding allele frequencies ranging from 0.005 to 0.469. The studied loci were in Hardy-Weinberg Equilibrium (HWE). Heterozygosity ranged from 0.602 to 0.867. The most polymorphic locus was Fibrinogen Alpha (FGA) chain which was also the most discriminating locus as expected. Neighbor Joining (NJ) tree and principal component analysis (PCA) plot clustered the Gorkhas with those of Nepal and other Tibeto-Burman population while lowlander Indian population formed separate cluster substantiating the closeness of the Gorkhas with the Tibeto-Burman linguistic phyla. Furthermore, the dataset of STR markers obtained in the study presents a valuable information source of STR DNA profiles from personnel for usage in disaster victim identification in military exigencies and adds to the Indian database of military soldiers and military hospital repository. PMID:27580933

  18. Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus)

    PubMed Central

    Taylor, Z S; Hoffman, S M G

    2014-01-01

    Dramatic changes in the North American landscape over the last 12 000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as FST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses. PMID:24448564

  19. Genetics affects choice of academic subjects as well as achievement

    PubMed Central

    Rimfeld, Kaili; Ayorech, Ziada; Dale, Philip S.; Kovas, Yulia; Plomin, Robert

    2016-01-01

    We have previously shown that individual differences in educational achievement are highly heritable throughout compulsory education. After completing compulsory education at age 16, students in England can choose to continue to study for two years (A-levels) in preparation for applying to university and they can freely choose which subjects to study. Here, for the first time, we show that choosing to do A-levels and the choice of subjects show substantial genetic influence, as does performance after two years studying the chosen subjects. Using a UK-representative sample of 6584 twin pairs, heritability estimates were 44% for choosing to do A-levels and 52–80% for choice of subject. Achievement after two years was also highly heritable (35–76%). The findings that DNA differences substantially affect differences in appetites as well as aptitudes suggest a genetic way of thinking about education in which individuals actively create their own educational experiences in part based on their genetic propensities. PMID:27310577

  20. Landscape structure, clonal propagation, and genetic diversity in Scandinavian populations of Arabidopsis lyrata (Brassicaceae).

    PubMed

    Gaudeul, Myriam; Stenøien, Hans K; Agren, Jon

    2007-07-01

    Colonization history, landscape structure, and environmental conditions may influence patterns of neutral genetic variation because of their effects on gene flow and reproductive mode. We compared variation at microsatellite loci within and among 26 Arabidopsis lyrata populations in two disjunct areas of its distribution in northern Europe (Norway and Sweden). The two areas probably share a common colonization history but differ in size (Norwegian range markedly larger than Swedish range), landscape structure (mountains vs. coast), and habitat conditions likely to affect patterns of gene flow and opportunities for sexual reproduction. Within-population genetic diversity was not related to latitude but was higher in Sweden than in Norway. Population differentiation was stronger among Norwegian than among Swedish populations (F(ST) = 0.23 vs. F(ST) = 0.18). The frequency of clonal propagation (proportion of identical multilocus genotypes) increased with decreasing population size, was higher in Norwegian than in Swedish populations, but was not related to altitude or substrate. Differences in genetic structure are discussed in relation to population characteristics and range size in the two areas. The results demonstrate that the possibility of clonal propagation should be considered when developing strategies for sampling and analyzing data in ecological and genetic studies of this emerging model species.

  1. Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Landraces have the potential to provide a reservoir of genetic diversity for crop improvement to combat the genetic erosion of the food supply. A landrace collection of the vitamin-rich specialty crop collard (Brassica oleracea var. viridis) was genetically characterized to assess its potential for ...

  2. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    PubMed Central

    Serrano, Magdalena; Calvo, Jorge H; Martínez, Marta; Marcos-Carcavilla, Ane; Cuevas, Javier; González, Carmen; Jurado, Juan J; de Tejada, Paloma Díez

    2009-01-01

    Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08) mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will facilitate the

  3. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes.

    PubMed

    Lequime, Sebastian; Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle; Lambrechts, Louis

    2016-06-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution.

  4. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes

    PubMed Central

    Fontaine, Albin; Ar Gouilh, Meriadeg; Moltini-Conclois, Isabelle

    2016-01-01

    Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. PMID:27304978

  5. Plant hybrid zones affect biodiversity: Tools for a genetic-based understanding of community structure

    SciTech Connect

    Whitham, T.G.; Martinsen, G.D.; Keim, P.; Floate, K.D.; Dungey, H.S. |; Potts, B.M.

    1999-03-01

    Plant hybrid zones are dynamic centers of ecological and evolutionary processes for plants and their associated communities. Studies in the wild and in gardens with synthetic crosses showed that hybrid eucalypts supports the greatest species richness and abundances of insect and fungal taxa. In an updated review of 152 case studies of taxa associated with diverse hybridizing systems, there were 43 (28%) cases of hybrids being more susceptible than their parent species, 7 (5%) resistant, 35 (23%) additive, 35 (23%) dominant, and 32 (21%) showed no response to hybridization. Thus, most taxa respond to hybrids in ways that result in equal or greater abundance, and hybrids tend to accumulate the taxa of their parent species. These studies suggest that genetic-based plant traits affect the distribution of many species and that the variation in hybrids can be used as tools to examine the genetic components of community structure and biodiversity.

  6. High level of genetic diversity among spelt germplasm revealed by microsatellite markers.

    PubMed

    Bertin, P; Grégoire, D; Massart, S; de Froidmont, D

    2004-12-01

    The genetic diversity of spelt (Triticum aestivum (L.) Thell. subsp. spelta (L.) Thell.) cultivated presently is very narrow. Although the germplasm collections of spelt are extensive, the related genetic knowledge is often lacking and makes their use for genetic improvement difficult. The genetic diversity and structure of the spelt gene pool held in gene banks was determined using 19 simple sequence repeat (SSR) markers applied to 170 spelt accessions collected from 27 countries and 4 continents. The genetic distances (1 - proportion of shared alleles) were calculated and an unweighted pair-group method with arithmetic averaging (UPGMA)-based dendrogram was generated. The genetic diversity was high: 259 alleles were found and the mean interaccession genetic distance was 0.782 +/- 0.141. The dendrogram demonstrated the much higher genetic diversity of spelt held in germplasm collections than in the currently used genotypes. Accessions with the same geographical origin often tended to cluster together. Those from the Middle East were isolated first. All but one of the Spanish accessions were found in a unique subcluster. Most accessions from eastern Europe clustered together, while those from northwestern Europe were divided into two subclusters. The accessions from Africa and North America were not separated from the European ones. This analysis demonstrates the extent of genetic diversity of spelts held in germplasm collections and should help to widen the genetic basis of cultivated spelt in future breeding programs.

  7. Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat.

    PubMed

    Bertin, Angeline; Gouin, Nicolas; Baumel, Alex; Gianoli, Ernesto; Serratosa, Juan; Osorio, Rodomiro; Manel, Stephanie

    2017-01-01

    Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens from five species (three common aquatic macroinvertebrate and two dominant plant species) that were genotyped for 396 amplified fragment length polymorphism loci. We also appraise the importance of neutral processes on SGDCs by investigating the influence of habitat fragmentation features. Significant positive SGDCs were detected for all five species (mean SGDC = 0.52 ± 0.05). While only a few outlier loci were detected in each species, they resulted in significant decreases in GD and in SGDCs. This supports the hypothesis that neutral processes drive species-genetic diversity relationships in high Andean wetlands. Unexpectedly, the effects on genetic diversity GD of the habitat fragmentation characteristics in this study increased with the presence of outlier loci in two species. Overall, our results reveal pitfalls in using habitat features to infer processes driving SGDCs and show that a few loci potentially under selection are enough to cause a significant downward bias in SGDC. Investigating confounding effects of outlier loci thus represents a useful approach to evidence the contribution of neutral processes on species-genetic diversity relationships.

  8. [Genetic polymorphisms commonly influencing efficacy of diverse addictive substances].

    PubMed

    Nishizawa, Daisuke; Ikeda, Kazutaka

    2014-04-01

    Opioids, such as morphine and fentanyl, are widely used as effective analgesics for the treatment of acute and chronic pain. In addition, the opioid system has a key role in the rewarding effects of morphine, ethanol, cocaine and various other drugs. The authors have focused on G-protein-activated inwardly rectifying potassium (GIRK) channel subunits, GIRK2 and GIRK3, that are important molecules in opioid transmission, and found that the single-nucleotide polymorphisms (SNPs) within the GIRK2 and GIRK3 gene regions were significantly associated with postoperative requirements of analgesics including opioids in patients who underwent abdominal surgery and mRNA expression of these genes in postmortem specimens, one of which was also associated with vulnerability to methamphetamine (METH) dependence. Further, by conducting a multistage genome-wide association study (GWAS) in healthy subjects, the authors found that genetic polymorphisms within a linkage disequilibrium block that spans 2q33.3-2q34 were strongly associated with the requirements for postoperative opioid analgesics after painful cosmetic surgery. The C allele of the best candidate SNP, rs2952768, was associated with more analgesic requirements, and consistent results were obtained in patients who underwent abdominal surgery. In addition, carriers of the C allele in this SNP exhibited less vulnerability to severe drug dependence in patients with methamphetamine dependence, alcohol dependence, and eating disorders and a lower 'Reward Dependence score on a personality questionnaire in healthy subjects. Furthermore, the C/C genotype of this SNP was significantly associated with the elevated expression of a neighboring gene, CREB1. The results show that SNPs in this locus are the most potent genetic factors associated with human opioid sensitivity known to date, affecting both the efficacy of opioid analgesics and liability to severe substance dependence. These outcomes provide valuable information for the

  9. Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world’s agro-ecological zones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countrie...

  10. Genotypic and Phenotypic Diversity Does Not Affect Productivity and Drought Response in Competitive Stands of Trifolium repens

    PubMed Central

    Huber, Heidrun; During, Heinjo J.; Bruine de Bruin, Fabienne; Vermeulen, Peter J.; Anten, Niels P. R.

    2016-01-01

    Clonal plants can form dense canopies in which plants of different genetic origin are competing for the uptake of essential resources. The competitive relationships among these clones are likely to be affected by extreme environmental conditions, such as prolonged drought spells, which are predicted to occur more frequently due to global climate change. This, in turn, may alter characteristics of the ecological system and its associated functioning. We hypothesized that the relative success of individual clones will depend on the size of the ramets as ramets with larger leaves and longer petioles (large ramets) were predicted to have a competitive advantage in terms of increased light interception over smaller-sized ramets. Under drier conditions the relative performances of genotypes were expected to change leading to a change in genotype ranking. We also hypothesized that increased genotypic and phenotypic diversity will increase stand performance and resistance to drought. These hypotheses and the mechanisms responsible for shifts in competitive relationships were investigated by subjecting genotypes of the important pasture legume Trifolium repens to competition with either genetically identical clones, genetically different but similarly sized clones, or genetically as well as morphologically different clones under well-watered and dry conditions. Competitive relationships were affected by ramet size with large genotypes outperforming small genotypes in diverse stands in terms of biomass production. However, large genotypes also produced relatively fewer ramets than small genotypes and could not benefit in terms of clonal reproduction from competing with smaller genotypes, indicating that evolutionary shifts in genotype composition will depend on whether ramet size or ramet number is under selection. In contrast to our hypotheses, diversity did not increase stand performance under different selection regimes and genotype ranking was hardly affected by soil

  11. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    PubMed Central

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm. PMID:21637550

  12. Molecular biology and genetic diversity of Rift Valley fever virus

    PubMed Central

    Ikegami, Tetsuro

    2013-01-01

    of invited papers in Antiviral Research on the genetic diversity of emerging viruses. PMID:22710362

  13. Molecular biology and genetic diversity of Rift Valley fever virus.

    PubMed

    Ikegami, Tetsuro

    2012-09-01

    of invited papers in Antiviral Research on the genetic diversity of emerging viruses.

  14. Genetic diversity and population structure of endangered Aquilaria malaccensis revealed potential for future conservation.

    PubMed

    Singh, Pradeep; Nag, Akshay; Parmar, Rajni; Ghosh, Sneha; Bhau, Brijmohan Singh; Sharma, Ram Kumar

    2015-12-01

    The endangered Aquilaria malaccensis,is an important plant with high economic values. Characterization of genetic diversity and population structure is receiving tremendous attention for effective conservation of genetic resources. Considering important repositories of biological diversity, the genetic relationships of 127 A. malaccensis accessions from 10 home gardens of three states of northeast India were assessed using amplified fragment length polymorphism (AFLP). Of the 1153 fragments amplified with four AFLP primer combinations, 916 (79.4%) were found to be polymorphic. Polymorphic information content (PIC) and marker index (MI) of each primer combination correlate significantly with the number of genotypes resolved. Overall, a high genetic diversity (avg. 71.85%) was recorded. Further, high gene flow (Nm: 3.37), low genetic differentiation (FST: 0.069) and high within population genetic variation (93%) suggests that most of the genetic diversity is restricted within population. Neighbour joining (NJ), principal coordinate analysis (PCoA) and Bayesian-based STRUCTURE grouped all the accessions in two clusters with significant intermixing between populations, therefore, revealed that two genetically distinct gene pools are operating in the A. malaccensis populations cultivated in home gardens. Based on the various diversity inferences, five diverse populations (JOH, FN, HLF, DHM and ITN) were identified, which can be potentially exploited to develop conservation strategies for A. malaccensis.

  15. Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant

    PubMed Central

    Gruber, Monica A M; Hoffmann, Benjamin D; Ritchie, Peter A; Lester, Philip J

    2012-01-01

    Many introduced species become invasive despite genetic bottlenecks that should, in theory, decrease the chances of invasion success. By contrast, population genetic bottlenecks have been hypothesized to increase the invasion success of unicolonial ants by increasing the genetic similarity between descendent populations, thus promoting co-operation. We investigated these alternate hypotheses in the unicolonial yellow crazy ant, Anoplolepis gracilipes, which has invaded Arnhem Land in Australia's Northern Territory. We used momentary abundance as a surrogate measure of invasion success, and investigated the relationship between A. gracilipes genetic diversity and its abundance, and the effect of its abundance on species diversity and community structure. We also investigated whether selected habitat characteristics contributed to differences in A. gracilipes abundance, for which we found no evidence. Our results revealed a significant positive association between A. gracilipes genetic diversity and abundance. Invaded communities were less diverse and differed in structure from uninvaded communities, and these effects were stronger as A. gracilipes abundance increased. These results contradict the hypothesis that genetic bottlenecks may promote unicoloniality. However, our A. gracilipes study population has diverged since its introduction, which may have obscured evidence of the bottleneck that would likely have occurred on arrival. The relative importance of genetic diversity to invasion success may be context dependent, and the role of genetic diversity may be more obvious in the absence of highly favorable novel ecological conditions. PMID:23139870

  16. Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger.

    PubMed

    Deu, Monique; Sagnard, F; Chantereau, J; Calatayud, C; Vigouroux, Y; Pham, J L; Mariac, C; Kapran, I; Mamadou, A; Gérard, B; Ndjeunga, J; Bezançon, G

    2010-05-01

    The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic erosion. Sorghum is the second staple cereal in Niger, a centre of diversity for this crop. Niger was submitted to recurrent drought period and to major social changes during these last decades. We report here on a spatio-temporal analysis of sorghum genetic diversity, conducted in 71 villages covering the rainfall gradient and range of agro-ecological conditions in Niger's agricultural areas. We used 28 microsatellite markers and applied spatial and genetic clustering methods to investigate change in genetic diversity over a 26-year period (1976-2003). Global genetic differentiation between the two collections was very low (F (st) = 0.0025). Most of the spatial clusters presented no major differentiation, as measured by F (st), and showed stability or an increase in allelic richness, except for two of them located in eastern Niger. The genetic clusters identified by Bayesian analysis did not show a major change between the two collections in the distribution of accessions between them or in their spatial location. These results suggest that farmers' management has globally preserved sorghum genetic diversity in Niger.

  17. Genetic diversity of a newly established population of golden eagles on the Channel Islands, California

    USGS Publications Warehouse

    Sonsthagen, Sarah A.; Coonan, Timothy J.; Latta, Brian C.; Sage, George K.; Talbot, Sandra L.

    2012-01-01

    Gene flow can have profound effects on the genetic diversity of a founding population depending on the number and relationship among colonizers and the duration of the colonization event. Here we used data from nuclear microsatellite and mitochondrial DNA control region loci to assess genetic diversity in golden eagles of the recently colonized Channel Islands, California. Genetic diversity in the Channel Island population was low, similar to signatures observed for other recent colonizing island populations. Differences in levels of genetic diversity and structure observed between mainland California and the islands suggests that few individuals were involved in the initial founding event, and may have comprised a family group. The spatial genetic structure observed between Channel Island and mainland California golden eagle populations across marker types, and genetic signature of population decline observed for the Channel Island population, suggest a single or relatively quick colonization event. Polarity in gene flow estimates based on mtDNA confirm an initial colonization of the Channel Islands by mainland golden eagles, but estimates from microsatellite data suggest that golden eagles on the islands were dispersing more recently to the mainland, possibly after reaching the carrying capacity of the island system. These results illustrate the strength of founding events on the genetic diversity of a population, and confirm that changes to genetic diversity can occur within just a few generations.

  18. Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations.

    PubMed

    Melka, M G; Sargolzaei, M; Miglior, F; Schenkel, F

    2013-02-01

    The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS.

  19. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    USGS Publications Warehouse

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  20. Genetic and non-genetic factors affecting morphometry of Sirohi goats

    PubMed Central

    Dudhe, S. D.; Yadav, S. B. S.; Nagda, R. K.; Pannu, Urmila; Gahlot, G. C.

    2015-01-01

    Aim: The aim was to estimate genetic and non-genetic factors affecting morphometric traits of Sirohi goats under field condition. Materials and Methods: The detailed information of all animals on body measurements at birth, 3, 6, 9, and 12 months of age was collected from farmer’s flock under field condition born during 2007-2013 to analyze the effect of genetic and non-genetic factors. The least squares maximum likelihood program was used to estimate genetic and non-genetic parameters affecting morphometric traits. Results and Discussion: Effect of sire, cluster, year of birth, and sex was found to be highly significant (p<0.01) on all three morphometric traits, parity was highly significant (p<0.01) for body height (BH) and body girth (BG) at birth. The h2 estimates for morphometric traits ranged among 0.528±0.163 to 0.709±0.144 for BH, 0.408±0.159 to 0.605±0.192 for body length (BL), and 0.503±0.197 to 0.695±0.161 for BG. Conclusion: The effect of sire was highly significant (p<0.01) and also h² estimate of all morphometric traits were medium to high; therefore, it could be concluded on the basis of present findings that animals with higher body measurements at initial phases of growth will perform better with respect to even body weight traits at later stages of growth. PMID:27047043

  1. Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop.

    PubMed

    Fregene, M A; Suarez, M; Mkumbira, J; Kulembeka, H; Ndedya, E; Kulaya, A; Mitchel, S; Gullberg, U; Rosling, H; Dixon, A G O; Dean, R; Kresovich, S

    2003-10-01

    Cassava (Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and Nigeria) and the Neotropics (Brazil, Colombia, Peru, Venezuela, Guatemala, Mexico and Argentina). Average gene diversity (i.e., genetic diversity) was high in all countries, with an average heterozygosity of 0.5358 +/- 0.1184. Although the highest was found in Brazilian and Colombian accessions, genetic diversity in Neotropical and African materials is comparable. Despite the low level of differentiation [F(st)(theta) = 0.091 +/- 0.005] found among country samples, sufficient genetic distance (1-proportion of shared alleles) existed between individual genotypes to separate African from Neotropical accessions and to reveal a more pronounced substructure in the African landraces. Forces shaping differences in allele frequency at SSR loci and possibly counterbalancing successive founder effects involve probably spontaneous recombination, as assessed by parent-offspring relationships, and farmer-selection for adaptation.

  2. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

    PubMed Central

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A.; Catenacci, Daniel V. T.; Hudson, Richard R.; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-01-01

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 “polymorphic” SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors. PMID:26561581

  3. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution.

    PubMed

    Ling, Shaoping; Hu, Zheng; Yang, Zuyu; Yang, Fang; Li, Yawei; Lin, Pei; Chen, Ke; Dong, Lili; Cao, Lihua; Tao, Yong; Hao, Lingtong; Chen, Qingjian; Gong, Qiang; Wu, Dafei; Li, Wenjie; Zhao, Wenming; Tian, Xiuyun; Hao, Chunyi; Hungate, Eric A; Catenacci, Daniel V T; Hudson, Richard R; Li, Wen-Hsiung; Lu, Xuemei; Wu, Chung-I

    2015-11-24

    The prevailing view that the evolution of cells in a tumor is driven by Darwinian selection has never been rigorously tested. Because selection greatly affects the level of intratumor genetic diversity, it is important to assess whether intratumor evolution follows the Darwinian or the non-Darwinian mode of evolution. To provide the statistical power, many regions in a single tumor need to be sampled and analyzed much more extensively than has been attempted in previous intratumor studies. Here, from a hepatocellular carcinoma (HCC) tumor, we evaluated multiregional samples from the tumor, using either whole-exome sequencing (WES) (n = 23 samples) or genotyping (n = 286) under both the infinite-site and infinite-allele models of population genetics. In addition to the many single-nucleotide variations (SNVs) present in all samples, there were 35 "polymorphic" SNVs among samples. High genetic diversity was evident as the 23 WES samples defined 20 unique cell clones. With all 286 samples genotyped, clonal diversity agreed well with the non-Darwinian model with no evidence of positive Darwinian selection. Under the non-Darwinian model, MALL (the number of coding region mutations in the entire tumor) was estimated to be greater than 100 million in this tumor. DNA sequences reveal local diversities in small patches of cells and validate the estimation. In contrast, the genetic diversity under a Darwinian model would generally be orders of magnitude smaller. Because the level of genetic diversity will have implications on therapeutic resistance, non-Darwinian evolution should be heeded in cancer treatments even for microscopic tumors.

  4. Environmental and genetic factors affecting cow survival of Israeli Holsteins.

    PubMed

    Weller, J I; Ezra, E

    2015-01-01

    The objectives were to investigate the effects of various environmental factors that may affect herd-life of Israeli Holsteins, including first-calving age and season, calving ease, number of progeny born, and service sire for first calving in complete and truncated records; and to estimate heritabilities and genetic correlations between herd-life and the other traits included in the Israeli breeding index. The basic data set consisted of 590,869 cows in milk recording herds with first freshening day between 1985 and at least 8 yr before the cut-off date of September 15, 2013. Herd-life was measured as days from first calving to culling. The phenotypic and genetic trends for herd-life were 5.7 and 16.8d/yr. The genetic trend was almost linear, whereas the phenotypic trend showed 4 peaks and 3 valleys. Cows born in February and March had the shortest herd-life, whereas cows born in September had the longest herd-life. Herd-life was maximal with calving age of 23mo, which is 1mo less than the mean calving age, and minimal at 19 and 31mo of calving age. Dystocia and twinning on first-parity calving reduced herd-life by approximately180 and 120d, but the interaction effect increased herd-life by 140d. Heritability for herd-life was 0.14. Despite the fact that the service sire effect was significant in the fixed model analysis, service sire effect accounted for <0.05% of the total variance. In the analysis of 1,431,938 truncated records, the effects of dystocia and twinning rate were very similar but less than 50% of the effects found in the analysis of complete records. Pregnancy at the truncation date increased expected herd-life by 432d. The correlation between actual herd-life and predicted herd-life based on truncated records was 0.44. Genetic correlations between the truncated records and actual herd-life were 0.75 for records truncated after 6mo but approached unity for records truncated after 3 yr. The genetic correlations of herd-life with first-parity milk

  5. Spatial Genetic Structure and Clonal Diversity in an Alpine Population of Salix herbacea (Salicaceae)

    PubMed Central

    Reisch, Christoph; Schurm, Sophia; Poschlod, Peter

    2007-01-01

    Background and Aims Many alpine plant species combine clonal and sexual reproduction to minimize the risks of flowering and seed production in high mountain regions. The spatial genetic structure and diversity of these alpine species is strongly affected by different clonal strategies (phalanx or guerrilla) and the proportion of generative and vegetative reproduction. Methods The clonal structure of the alpine plant species Salix herbacea was investigated in a 3 × 3 m plot of an alpine meadow using microsatellite (simple sequence repeat; SSR) analysis. The data obtained were compared with the results of a random amplified polymorphic DNA (RAPD) analysis. Key Results SSR analysis, based on three loci and 16 alleles, revealed 24 different genotypes and a proportion of distinguishable genotypes of 0·18. Six SSR clones were found consisting of at least five samples, 17 clones consisting of more than two samples and seven single genotypes. Mean clone size comprising at least five samples was 0·96 m2, and spatial autocorrelation analysis showed strong similarity of samples up to 130 cm. RAPD analysis revealed a higher level of clonal diversity but a comparable number of larger clones and a similar spatial structure. Conclusions The spatial genetic structure as well as the occurrence of single genotypes revealed in this study suggests both clonal and sexual propagation and repeated seedling recruitment in established populations of S. herbacea and is thus suggestive of a relaxed phalanx strategy. PMID:17242040

  6. Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change.

    PubMed

    Lopes, Marta S; El-Basyoni, Ibrahim; Baenziger, Peter S; Singh, Sukhwinder; Royo, Conxita; Ozbek, Kursad; Aktas, Husnu; Ozer, Emel; Ozdemir, Fatih; Manickavelu, Alagu; Ban, Tomohiro; Vikram, Prashant

    2015-06-01

    Climate change has generated unpredictability in the timing and amount of rain, as well as extreme heat and cold spells that have affected grain yields worldwide and threaten food security. Sources of specific adaptation related to drought and heat, as well as associated breeding of genetic traits, will contribute to maintaining grain yields in dry and warm years. Increased crop photosynthesis and biomass have been achieved particularly through disease resistance and healthy leaves. Similarly, sources of drought and heat adaptation through extended photosynthesis and increased biomass would also greatly benefit crop improvement. Wheat landraces have been cultivated for thousands of years under the most extreme environmental conditions. They have also been cultivated in lower input farming systems for which adaptation traits, particularly those that increase the duration of photosynthesis, have been conserved. Landraces are a valuable source of genetic diversity and specific adaptation to local environmental conditions according to their place of origin. Evidence supports the hypothesis that landraces can provide sources of increased biomass and thousand kernel weight, both important traits for adaptation to tolerate drought and heat. Evaluation of wheat landraces stored in gene banks with highly beneficial untapped diversity and sources of stress adaptation, once characterized, should also be used for wheat improvement. Unified development of databases and promotion of data sharing among physiologists, pathologists, wheat quality scientists, national programmes, and breeders will greatly benefit wheat improvement for adaptation to climate change worldwide.

  7. Analysis of Fungicide Sensitivity and Genetic Diversity among Colletotrichum Species in Sweet Persimmon

    PubMed Central

    Gang, Geun-Hye; Cho, Hyun Ji; Kim, Hye Sun; Kwack, Yong-Bum; Kwak, Youn-Sig

    2015-01-01

    Anthracnose, caused by Colletotrichum gloeosporioides (C. gloeosporioides; Teleomorph: Glomerella cingulata), is the most destructive disease that affects sweet persimmon production worldwide. However, the biology, ecology, and genetic variations of C. gloeosporioides remain largely unknown. Therefore, in this study, the development of fungicide resistance and genetic diversity among an anthracnose pathogen population with different geographical origins and the exposure of this population to different cultivation strategies were investigated. A total of 150 pathogen isolates were tested in fungicide sensitivity assays. Five of the tested fungicides suppressed mycelial pathogen growth effectively. However, there were significant differences in the sensitivities exhibited by the pathogen isolates examined. Interestingly, the isolates obtained from practical management orchards versus organic cultivation orchards showed no differences in sensitivity to the same fungicide. PCR-restriction fragment length polymorphism (RFLP) analyses were performed to detect internal transcribed spacer regions and the β-tubulin and glutamine synthetase genes of the pathogens examined. Both the glutamine synthetase and β-tubulin genes contained a complex set of polymorphisms. Based on these results, the pathogens isolated from organic cultivation orchards were found to have more diversity than the isolates obtained from the practical management orchards. PMID:26060430

  8. Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae)

    PubMed Central

    Pan, Yuezhi; Wang, Xueqin; Sun, Guiling; Li, Fusheng; Gong, Xun

    2016-01-01

    Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis. PMID:27846268

  9. Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral.

    PubMed

    Nunes, F; Norris, R D; Knowlton, N

    2009-10-01

    Limited dispersal and connectivity in marine organisms can have negative fitness effects in populations that are small and isolated, but reduced genetic exchange may also promote the potential for local adaptation. Here, we compare the levels of genetic diversity and connectivity in the coral Montastraea cavernosa among both central and peripheral populations throughout its range in the Atlantic. Genetic data from one mitochondrial and two nuclear loci in 191 individuals show that M. cavernosa is subdivided into three genetically distinct regions in the Atlantic: Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern Tropical Atlantic (West Africa). Within each region, populations have similar allele frequencies and levels of genetic diversity; indeed, no significant differentiation was found between populations separated by as much as 3000 km, suggesting that this coral species has the ability to disperse over large distances. Gene flow within regions does not, however, translate into connectivity across the entire Atlantic. Instead, substantial differences in allele frequencies across regions suggest that genetic exchange is infrequent between the Caribbean, Brazil and West Africa. Furthermore, markedly lower levels of genetic diversity are observed in the Brazilian and West African populations. Genetic diversity and connectivity may contribute to the resilience of a coral population to disturbance. Isolated peripheral populations may be more vulnerable to human impacts, disease or climate change relative to those in the genetically diverse Caribbean-North Atlantic region.

  10. Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

    PubMed

    Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

    2016-04-30

    Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures.

  11. Evaluation of fire recurrence effect on genetic diversity in maritime pine (Pinus pinaster Ait.) stands using Inter-Simple Sequence Repeat profiles.

    PubMed

    Lucas-Borja, M E; Ahrazem, O; Candel-Pérez, D; Moya, D; Fonseca, T; Hernández Tecles, E; De Las Heras, J; Gómez-Gómez, L

    2016-12-01

    The management of maritime pine in fire-prone habitats is a challenging task and fine-scale population genetic analyses are necessary to check if different fire recurrences affect genetic variability. The objective of this study was to assess the effect of fire recurrence on maritime pine genetic diversity using inter-simple sequence repeat markers (ISSR). Three maritime pine (Pinus pinaster Ait.) populations from Northern Portugal were chosen to characterize the genetic variability among populations. In relation to fire recurrence, Seirós population was affected by fire both in 1990 and 2005 whereas Vila Seca-2 population was affected by fire just in 2005. The Vila Seca-1 population has been never affected by fire. Our results showed the highest Nei's genetic diversity (He=0.320), Shannon information index (I=0.474) and polymorphic loci (PPL=87.79%) among samples from twice burned populations (Seirós site). Thus, fire regime plays an important role affecting genetic diversity in the short-term, although not generating maritime pine genetic erosion.

  12. Genetic diversity of coastal bottlenose dolphins revealed by structurally and functionally diverse hemoglobins.

    PubMed

    Remington, Nicole; Stevens, Robert D; Wells, Randall S; Holn, Aleta; Dhungana, Suraj; Taboy, Celine H; Crumbliss, Alvin L; Henkens, Robert; Bonaventura, Celia

    2007-08-15

    Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhances oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their alpha and beta globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community.

  13. A natural genetic polymorphism affects retroactive interference in Drosophila melanogaster

    PubMed Central

    Reaume, Christopher J.; Sokolowski, Marla B.; Mery, Frederic

    2011-01-01

    As environments change, animals update their internal representations of the external world. New information about the environment is learned and retained whereas outdated information is disregarded or forgotten. Retroactive interference (RI) occurs when the retrieval of previously learned information is less available owing to the acquisition of recently acquired information. Even though RI is thought to be a major cause of forgetting, its functional significance is still under debate. We find that natural allelic variants of the Drosophila melanogaster foraging gene known to affect rover and sitter behaviour differ in RI. More specifically, rovers who were previously shown to experience greater environmental heterogeneity while foraging display RI whereas sitters do not. Rover responses are biased towards more recent learning events. These results provide an ecological context to investigate the function of forgetting via RI and a suitable genetic model organism to address the evolutionary relevance of cognitive tasks. PMID:20667877

  14. Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity.

    PubMed

    Calusinska, Magdalena; Marynowska, Martyna; Goux, Xavier; Lentzen, Esther; Delfosse, Philippe

    2016-04-01

    Although viruses are not the key players of the anaerobic digestion process, they may affect the dynamics of bacterial and archaeal populations involved in biogas production. Until now viruses have received very little attention in this specific habitat; therefore, as a first step towards their characterization, we optimized a virus filtration protocol from anaerobic sludge. Afterwards, to assess dsDNA and RNA viral diversity in sludge samples from nine different reactors fed either with waste water, agricultural residues or solid municipal waste plus agro-food residues, we performed metagenomic analyses. As a result we showed that, while the dsDNA viromes (21 assigned families in total) were dominated by dsDNA phages of the order Caudovirales, RNA viruses (14 assigned families in total) were less diverse and were for the main part plant-infecting viruses. Interestingly, less than 2% of annotated contigs were assigned as putative human and animal pathogens. Our study greatly extends the existing view of viral genetic diversity in methanogenic reactors and shows that these viral assemblages are distinct not only among the reactor types but also from nearly 30 other environments already studied, including the human gut, fermented food, deep sea sediments and other aquatic habitats.

  15. Population Genetic Diversity in the Australian ‘Seascape’: A Bioregion Approach

    PubMed Central

    Pope, Lisa C.; Riginos, Cynthia; Ovenden, Jennifer; Keyse, Jude; Blomberg, Simon P.

    2015-01-01

    Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitude squared. Removing region as an explanatory variable greatly reduced model performance (delta DIC 23.4). Several bioregions were identified as possessing notably high genetic diversity. Genetic diversity increased towards the equator with a ‘hump’ in diversity across the range studied (−9.4 to −43.7°S). Our results suggest that factors correlated with both region and latitude play a role in shaping intra-specific genetic diversity, and that bioregion can be a useful management unit for intra-specific as well as species biodiversity. Our novel statistical model should prove useful for future analyses of within species genetic diversity at broad taxonomic and geographic scales. PMID:26375711

  16. Genetic diversity of some Mediterranean populations of the cultivated alfalfa (Medicago sativa L.) using SSR markers.

    PubMed

    Touil, L; Guesmi, F; Fares, K; Zagrouba, C; Ferchichi, A

    2008-08-01

    This species study was to investigate the differentiation level among 26 populations in which 12 are locals originating from the Tunisian South and 14 introduced from Italy, Austerely, France and Morocco with two SSR markers. These highly polymorphic and co dominant markers, together with recent population genetic statistic extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 8 and 9. The genetic similarity between these various populations is estimated by the index of Rogers and Tanimoto. Genetic diversity is analysed by two statistical procedures: Hierarchical classification and Correspondence Factorial Analysis (CFA). Four large groups were obtained.

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

    PubMed Central

    2016-01-01

    Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest. PMID:26871719

  18. Genetic diversity and population structure of Plasmodium vivax isolates from Sudan, Madagascar, French Guiana and Armenia.

    PubMed

    Menegon, Michela; Durand, Patrick; Menard, Didier; Legrand, Eric; Picot, Stéphane; Nour, Bakri; Davidyants, Vladimir; Santi, Flavia; Severini, Carlo

    2014-10-01

    Polymorphic genetic markers and especially microsatellite analysis can be used to investigate multiple aspects of the biology of Plasmodium species. In the current study, we characterized 7 polymorphic microsatellites in a total of 281 Plasmodium vivax isolates to determine the genetic diversity and population structure of P. vivax populations from Sudan, Madagascar, French Guiana, and Armenia. All four parasite populations were highly polymorphic with 3-32 alleles per locus. Mean genetic diversity values was 0.83, 0.79, 0.78 and 0.67 for Madagascar, French Guiana, Sudan, and Armenia, respectively. Significant genetic differentiation between all four populations was observed.

  19. Analyses of genetic diversity in five Canadian dairy breeds using pedigree data.

    PubMed

    Melka, M G; Stachowicz, K; Miglior, F; Schenkel, F S

    2013-12-01

    The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within-breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised.

  20. Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.

    PubMed

    Haber, Marc; Mezzavilla, Massimo; Bergström, Anders; Prado-Martinez, Javier; Hallast, Pille; Saif-Ali, Riyadh; Al-Habori, Molham; Dedoussis, George; Zeggini, Eleftheria; Blue-Smith, Jason; Wells, R Spencer; Xue, Yali; Zalloua, Pierre A; Tyler-Smith, Chris

    2016-12-01

    Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%-30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

  1. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

    PubMed Central

    Dinarti, Diny; Susilo, Agung W.; Meinhardt, Lyndel W.; Ji, Kun; Motilal, Lambert A.; Mischke, Sue; Zhang, Dapeng

    2015-01-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  2. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-12-03

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability.

  3. Application of restriction site amplified polymorphism (RSAP) to genetic diversity in Saccharina japonica

    NASA Astrophysics Data System (ADS)

    Zhao, Cui; Liu, Cui; Li, Wei; Chi, Shan; Feng, Rongfang; Liu, Tao

    2013-07-01

    Restriction site amplified polymorphism (RSAP) was used, for the first time, to analyze the genetic structure and diversity of four, mainly cultivated, varieties of the brown alga, Saccharina japonica. Eighty-eight samples from varieties " Rongfu ", " Fujian ", " Ailunwan " and " Shengchanzhong " were used for the genetic analyses. One hundred and ninety-eight bands were obtained using eight combinations of primers. One hundred and ninety-one (96.46%) were polymorphic bands. Nei's genetic diversity was 0.360, and the coefficient of genetic differentiation was 0.357. No inbreeding-type recession was found in the four brown alga varieties and the results of the " Ailunwan " variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program. Genetic diversity and cluster analyses results were consistent with these genetic relationships. The results show the RSAP method is suitable for genetic analysis. Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.

  4. Genetic diversity and structure of the threatened species Sinopodophyllum hexandrum (Royle) Ying.

    PubMed

    Liu, W; Wang, J; Yin, D X; Yang, M; Wang, P; Han, Q S; Ma, Q Q; Liu, J J; Wang, J X

    2016-06-10

    Sinopodophyllum hexandrum is an important medicinal plant that has been listed as an endangered species, making the conservation of its genetic diversity a priority. Therefore, the genetic diversity and population structure of S. hexandrum was investigated through inter-simple sequence repeat analysis of eight natural populations. Eleven selected primers generated 141 discernible fragments. The percentage of polymorphic bands was 37.59% at the species level, and 7.66-24.32% at the population level. Genetic diversity of S. hexandrum was low within populations (average HE = 0.0366), but higher at the species level (HE = 0.0963). Clear structure and high genetic differentiation were detected between populations using unweighted pair groups mean arithmetic and principle coordinate analysis. Clustering approaches clustered the eight sampled populations into three major groups, and AMOVA confirmed there to be significant variation between populations (63.27%). Genetic differentiation may have arisen through limited gene flow (Nm = 0.3317) in this species. Isolation by distance among populations was determined by comparing genetic distance versus geographical distance using the Mantel test. The results revealed no correlation between spatial pattern and geographic location. Given the low within-population genetic diversity, high differentiation among populations, and the increasing anthropogenic pressure on this species, in situ conservation measures, in addition to sampling and ex situ preservation, are recommended to preserve S. hexandrum populations and to retain their genetic diversity.

  5. Genetic Diversity in Cytokines Associated with Immune Variation and Resistance to Multiple Pathogens in a Natural Rodent Population

    PubMed Central

    Turner, Andrew K.; Begon, Mike; Jackson, Joseph A.; Bradley, Janette E.; Paterson, Steve

    2011-01-01

    Pathogens are believed to drive genetic diversity at host loci involved in immunity to infectious disease. To date, studies exploring the genetic basis of pathogen resistance in the wild have focussed almost exclusively on genes of the Major Histocompatibility Complex (MHC); the role of genetic variation elsewhere in the genome as a basis for variation in pathogen resistance has rarely been explored in natural populations. Cytokines are signalling molecules with a role in many immunological and physiological processes. Here we use a natural population of field voles (Microtus agrestis) to examine how genetic diversity at a suite of cytokine and other immune loci impacts the immune response phenotype and resistance to several endemic pathogen species. By using linear models to first control for a range of non-genetic factors, we demonstrate strong effects of genetic variation at cytokine loci both on host immunological parameters and on resistance to multiple pathogens. These effects were primarily localized to three cytokine genes (Interleukin 1 beta (Il1b), Il2, and Il12b), rather than to other cytokines tested, or to membrane-bound, non-cytokine immune loci. The observed genetic effects were as great as for other intrinsic factors such as sex and body weight. Our results demonstrate that genetic diversity at cytokine loci is a novel and important source of individual variation in immune function and pathogen resistance in natural populations. The products of these loci are therefore likely to affect interactions between pathogens and help determine survival and reproductive success in natural populations. Our study also highlights the utility of wild rodents as a model of ecological immunology, to better understand the causes and consequences of variation in immune function in natural populations including humans. PMID:22039363

  6. Imidacloprid induces changes in the structure, genetic diversity and catabolic activity of soil microbial communities.

    PubMed

    Cycoń, Mariusz; Markowicz, Anna; Borymski, Sławomir; Wójcik, Marcin; Piotrowska-Seget, Zofia

    2013-12-15

    This is the first report describing the effect of imidacloprid applied at field rate (FR, 1 mg/kg of soil) and 10 times the FR (10*FR, 10 mg/kg of soil) on the structural, genetic and physiological diversity of soil bacterial community as determined by the phospholipid fatty acid (PLFA), the denaturing gradient gel electrophoresis (DGGE), and the community level physiological profile (CLPP) approaches. PLFA profiles showed that imidacloprid significantly shifted the microbial community structure and decreased the biomass of the total, bacterial and fungal PLFAs, however, this effect was transient at the FR dosage. The alterations in DGGE patterns caused by imidacloprid application, confirmed considerable changes in the overall richness and diversity of dominant bacteria. Although, as a result of imidacloprid application, the metabolic activity of microbial communities was generally lower, the richness and functional biodiversity of the soil microbial community were not negatively affected. In general, the analysis of the variance indicated that the measured parameters were significantly affected by treatment and the incubation time, however, the incubation time effect explained most of the observed variance. Imidacloprid degradation and the appearance of some new bands in DGGE profiles suggest the evolution of bacteria capable of degrading imidacloprid among indigenous microflora.

  7. Does antiepileptogenesis affect sleep in genetic epileptic rats?

    PubMed

    van Luijtelaar, Gilles; Wilde, Matthias; Citraro, Rita; Scicchitano, Francesca; van Rijn, Clementina

    2012-07-01

    Recently it was established that early long lasting treatment with the anti-absence drug ethosuximide (ETX) delays the occurrence of absences and reduces depressive-like symptoms in a genetic model for absence epilepsy, rats of the WAG/Rij strain. Here it is investigated whether anti-epileptogenesis (chronic treatments with ETX for 2 and 4 months) affects REM sleep in this model. Four groups of weaned male WAG/Rij rats were treated with ETX for 4 months, two groups for 2 months (at 2-3 and 4-5 months of age), the fourth group was untreated. Next, the rats were recorded 6 days after the last day of the treatment for 22.5 h. Non-REM sleep and REM sleep parameters and delta power were analyzed in four characteristic and representative hours of the recoding period. Four months treatment with ETX reduced the amount of REM sleep and REM sleep as percentage of total sleep time. Other sleep parameters were not affected by the treatment. Clear differences between the various hours of the light-dark phase in amounts of non-REM and REM sleep and delta power were found, in line with commonly reported circadian sleep patterns. It can be concluded that the reduction of REM sleep is unique for the early and long lasting chronic treatment. The outcomes may explain our earlier finding that a reduction of REM sleep might alleviate depressive like symptoms.

  8. Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers.

    PubMed

    Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F

    2014-09-26

    Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701). The accessions with the highest genetic diversity (effective number of alleles, NE = 1.609; Nei's genetic diversity, H = 0.372; Shannon information index, I = 0.556) were from Italy. The richest genetic diversity was revealed in a chicory line (NE = 1.478, H = 0.289, I = 0.443) among the 3 types (line, wild, and cultivar). The chicory genetic structure of 8 geographical groups showed that the genetic differentiation coefficient (GST) was 14.20% and the number of immigrants per generation (Nm) was 3.020. A GST of 6.80% and an Nm of 6.853 were obtained from different types. This observation suggests that these chicory lines, especially those from the Mediterranean region, have potential for providing rich genetic resources for further breeding programs, that the chicory genetic structure among different countries obviously differs with a certain amount of gene flow, and that SRAP markers could be applied to analyze genetic relationships and classifications of Cichorium intybus and C. endivia.

  9. Genetic diversity and domestication origin of tea plant Camellia taliensis (Theaceae) as revealed by microsatellite markers

    PubMed Central

    2014-01-01

    Background Tea is one of the most popular beverages in the world. Many species in the Thea section of the Camellia genus can be processed for drinking and have been domesticated. However, few investigations have focused on the genetic consequence of domestication and geographic origin of landraces on tea plants using credible wild and planted populations of a single species. Here, C. taliensis provides us with a unique opportunity to explore these issues. Results Fourteen nuclear microsatellite loci were employed to determine the genetic diversity and domestication origin of C. taliensis, which were represented by 587 individuals from 25 wild, planted and recently domesticated populations. C. taliensis showed a moderate high level of overall genetic diversity. The greater reduction of genetic diversity and stronger genetic drift were detected in the wild group than in the recently domesticated group, indicating the loss of genetic diversity of wild populations due to overexploitation and habitat fragmentation. Instead of the endangered wild trees, recently domesticated individuals were used to compare with the planted trees for detecting the genetic consequence of domestication. A little and non-significant reduction in genetic diversity was found during domestication. The long life cycle, selection for leaf traits and gene flow between populations will delay the emergence of bottleneck in planted trees. Both phylogenetic and assignment analyses suggested that planted trees may have been domesticated from the adjacent central forest of western Yunnan and dispersed artificially to distant places. Conclusions This study contributes to the knowledge about levels and distribution of genetic diversity of C. taliensis and provides new insights into genetic consequence of domestication and geographic origin of planted trees of this species. As an endemic tea source plant, wild, planted and recently domesticated C. taliensis trees should all be protected for their unique

  10. Genetic effects of habitat restoration in the Laurentian Great Lakes: an assessment of lake sturgeon origin and genetic diversity

    USGS Publications Warehouse

    Jamie Marie Marranca,; Amy Welsh,; Roseman, Edward F.

    2015-01-01

    Lake sturgeon (Acipenser fulvescens) have experienced significant habitat loss, resulting in reduced population sizes. Three artificial reefs were built in the Huron-Erie corridor in the Great Lakes to replace lost spawning habitat. Genetic data were collected to determine the source and numbers of adult lake sturgeon spawning on the reefs and to determine if the founder effect resulted in reduced genetic diversity. DNA was extracted from larval tail clips and 12 microsatellite loci were amplified. Larval genotypes were then compared to 22 previously studied spawning lake sturgeon populations in the Great Lakes to determine the source of the parental population. The effective number of breeders (Nb) was calculated for each reef cohort. The larval genotypes were then compared to the source population to determine if there were any losses in genetic diversity that are indicative of the founder effect. The St. Clair and Detroit River adult populations were found to be the source parental population for the larvae collected on all three artificial reefs. There were large numbers of contributing adults relative to the number of sampled larvae. There was no significant difference between levels of genetic diversity in the source population and larval samples from the artificial reefs; however, there is some evidence for a genetic bottleneck in the reef populations likely due to the founder effect. Habitat restoration in the Huron-Erie corridor is likely resulting in increased habitat for the large lake sturgeon population in the system and in maintenance of the population's genetic diversity.

  11. Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers.

    PubMed

    Ulloa, Odeth; Ortega, Fernando; Campos, Hugo

    2003-08-01

    Red clover is an important forage legume species for temperate regions and very little is known about the genetic organization of its breeding populations. We used random amplified polymorphic DNA (RAPD) genetic markers to address the genetic diversity and the distribution of variation in 20 breeding populations and cultivars from Chile, Argentina, Uruguay, and Switzerland. Genetic distances were calculated for all possible pairwise combinations. A high level of polymorphism was found and the proportion of polymorphic loci across populations was 74.2%. A population derived from a non-certified seedlot displayed a higher proportion of polymorphic loci than its respective certified seedlot. Gene diversity values and population genetics parameters suggest that the populations analyzed are diverse. An analysis of molecular variance (AMOVA) revealed that the largest proportion of variation (80.4%) resides at the within population level. RAPD markers are a useful tool for red clover breeding programs. A dendrogram based on genetic distances divided the breeding populations analyzed into three distinct groups. The amount and partition of diversity observed can be of value in identifying the populations that parents of synthetic cultivars are derived from and to exploit the variation available in the populations analyzed.

  12. Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

  13. Multiple paternity or multiple queens: two routes to greater intracolonial genetic diversity in the eusocial Hymenoptera.

    PubMed

    Hughes, W O H; Ratnieks, F L W; Oldroyd, B P

    2008-07-01

    Understanding the evolution of multiple mating by females (polyandry) is an important question in behavioural ecology. Most leading explanations for polyandry by social insect queens are based upon a postulated fitness benefit from increased intracolonial genetic diversity, which also arises when colonies are headed by multiple queens (polygyny). An indirect test of the genetic diversity hypotheses is therefore provided by the relationship between polyandry and polygyny across species, which should be negative if the genetic diversity hypotheses are correct. Here, we conduct a powerful comparative investigation of the relationship between polyandry and polygyny for 241 species of eusocial Hymenoptera (ants, bees and wasps). We find a clear and significant negative relationship between polyandry and polygyny after controlling for phylogeny. These results strongly suggest that fitness benefits resulting from increased intracolonial genetic diversity have played an important role in the evolution of polyandry, and possibly polygyny, in social insects.

  14. Tetraploid Wheat Landraces in the Mediterranean Basin: Taxonomy, Evolution and Genetic Diversity

    PubMed Central

    Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.

    2012-01-01

    The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields. PMID:22615891

  15. Genetic diversity and geographical distribution of indigenous soybean-nodulating Bradyrhizobia in the United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The relationship of indigenous soybean-nodulating bradyrhizobial genetic diversity and geographical distribution in the United States of America (USA) were investigated using soil isolates from eight states (Michigan, Ohio, Kentucky, North Carolina, Alabama, Georgia, Florida and Louisiana) with thre...

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

    EPA Science Inventory

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

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

    PubMed

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

    2012-03-08

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

  18. Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

    PubMed Central

    Whitlock, Raj

    2014-01-01

    Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These

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

    USGS Publications Warehouse

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

    2010-01-01

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

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

    USGS Publications Warehouse

    Huff, D.D.; Miller, L.M.; Vondracek, B.

    2010-01-01

    Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

  1. Adaptability of non-genetic diversity in bacterial chemotaxis.

    PubMed

    Frankel, Nicholas W; Pontius, William; Dufour, Yann S; Long, Junjiajia; Hernandez-Nunez, Luis; Emonet, Thierry

    2014-10-03

    Bacterial chemotaxis systems are as diverse as the environments that bacteria inhabit, but how much environmental variation can cells tolerate with a single system? Diversification of a single chemotaxis system could serve as an alternative, or even evolutionary stepping-stone, to switching between multiple systems. We hypothesized that mutations in gene regulation could lead to heritable control of chemotactic diversity. By simulating foraging and colonization of E. coli using a single-cell chemotaxis model, we found that different environments selected for different behaviors. The resulting trade-offs show that populations facing diverse environments would ideally diversify behaviors when time for navigation is limited. We show that advantageous diversity can arise from changes in the distribution of protein levels among individuals, which could occur through mutations in gene regulation. We propose experiments to test our prediction that chemotactic diversity in a clonal population could be a selectable trait that enables adaptation to environmental variability.

  2. Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

    PubMed Central

    2010-01-01

    Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success. PMID:20698974

  3. Genetic diversity in two introduced biofouling amphipods (Amphipods valida and Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity

    EPA Science Inventory

    We investigated patterns of genetic diversity among invasive populations of A. valida and J. marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute...

  4. Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii).

    PubMed

    Morris, Katrina M; Wright, Belinda; Grueber, Catherine E; Hogg, Carolyn; Belov, Katherine

    2015-08-01

    The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in threatened species.

  5. Peripheral circadian clocks are diversely affected by adrenalectomy.

    PubMed

    Soták, M; Bryndová, J; Ergang, P; Vagnerová, K; Kvapilová, P; Vodička, M; Pácha, J; Sumová, A

    2016-01-01

    Glucocorticoids are considered to synchronize the rhythmicity of clock genes in peripheral tissues; however, the role of circadian variations of endogenous glucocorticoids is not well defined. In the present study, we examined whether peripheral circadian clocks were impaired by adrenalectomy. To achieve this, we tested the circadian rhythmicity of core clock genes (Bmal1, Per1-3, Cry1, RevErbα, Rora), clock-output genes (Dbp, E4bp4) and a glucocorticoid- and clock-controlled gene (Gilz) in liver, jejunum, kidney cortex, splenocytes and visceral adipose tissue (VAT). Adrenalectomy did not affect the phase of clock gene rhythms but distinctly modulated clock gene mRNA levels, and this effect was partially tissue-dependent. Adrenalectomy had a significant inhibitory effect on the level of Per1 mRNA in VAT, liver and jejunum, but not in kidney and splenocytes. Similarly, adrenalectomy down-regulated mRNA levels of Per2 in splenocytes and VAT, Per3 in jejunum, RevErbα in VAT and Dbp in VAT, kidney and splenocytes, whereas the mRNA amounts of Per1 and Per2 in kidney and Per3 in VAT and splenocytes were up-regulated. On the other hand, adrenalectomy had minimal effects on Rora and E4bp4 mRNAs. Adrenalectomy also resulted in decreased level of Gilz mRNA but did not alter the phase of its diurnal rhythm. Collectively, these findings suggest that adrenalectomy alters the mRNA levels of core clock genes and clock-output genes in peripheral organs and may cause tissue-specific modulations of their circadian profiles, which are reflected in changes of the amplitudes but not phases. Thus, the circulating corticosteroids are necessary for maintaining the high-amplitude rhythmicity of the peripheral clocks in a tissue-specific manner.

  6. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages

    PubMed Central

    Gaggiotti, Oscar E.; Treml, Eric A.; Wren, Johanna L. K.; Donovan, Mary K.; Toonen, Robert J.

    2016-01-01

    Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems. PMID:27122569

  7. Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR.

    PubMed

    Teixeira, Helena; Rodríguez-Echeverría, Susana; Nabais, Cristina

    2014-01-01

    Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe.

  8. Genetic Diversity and Differentiation of Juniperus thurifera in Spain and Morocco as Determined by SSR

    PubMed Central

    Teixeira, Helena; Rodríguez-Echeverría, Susana; Nabais, Cristina

    2014-01-01

    Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe. PMID:24533164

  9. Relationship between the genetic diversity of Artemisia halodendron and climatic factors

    NASA Astrophysics Data System (ADS)

    Huang, Wenda; Zhao, Xueyong; Zhao, Xin; Li, Yuqiang; Lian, Jie; Yun, Jianying

    2014-02-01

    Artemisia halodendron (Asteraceae) is a dominant sand-fixing semi-shrub species native to the Horqin Sandy Land of northeastern China. In this study, we evaluated levels of genetic variation within and among sampled A. halodendron populations from two different hydrothermal regions of the Horqin Sandy Land using inter-simple sequence repeat (ISSR) markers. We also investigated possible relationships between genetic diversity of this species and climatic factors. Our analysis revealed that A. halodendron is highly genetically diverse, with populations from a low hydrothermal level region having higher genetic diversity index values than those from a high hydrothermal level region. An analysis of molecular variation (AMOVA) revealed relatively high levels (>89.83%) of within-population genetic variation. Based on cluster analysis, the 13 studied A. halodendron populations can be clustered into two clades. Genetic diversities of all populations have been influenced by many climatic factors, and Nei's genetic diversity (h) is strongly correlated with annual temperature range (ART). These results have important implications for restoration and management of degraded ecosystems in arid and semi-arid areas.

  10. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    PubMed Central

    Gizaw, Solomon; Komen, Hans; Windig, Jack J; Hanotte, Olivier; van Arendonk, Johan AM

    2008-01-01

    Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers) and current merits (economic, ecological and cultural merits). Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04) as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83). We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan. PMID:18558075

  11. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages.

    PubMed

    Selkoe, Kimberly A; Gaggiotti, Oscar E; Treml, Eric A; Wren, Johanna L K; Donovan, Mary K; Toonen, Robert J

    2016-04-27

    Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems.

  12. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    PubMed

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  13. Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

    PubMed

    Lima, Jacqueline S; Ballesteros-Mejia, Liliana; Lima-Ribeiro, Matheus S; Collevatti, Rosane G

    2017-03-13

    The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled Ecological Niche Modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions. This article is protected by copyright. All rights reserved.

  14. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment.

    PubMed

    Yıldız, M; Koçak, M; Baloch, F S

    2015-09-08

    Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra.

  15. Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources

    PubMed Central

    van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A.; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I.

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at

  16. Mapping genetic diversity of cherimoya (Annona cherimola Mill.): application of spatial analysis for conservation and use of plant genetic resources.

    PubMed

    Zonneveld, Maarten van; Scheldeman, Xavier; Escribano, Pilar; Viruel, María A; Van Damme, Patrick; Garcia, Willman; Tapia, César; Romero, José; Sigueñas, Manuel; Hormaza, José I

    2012-01-01

    There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value