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Sample records for genetic diversity relationships

  1. Analysis on genetic diversity and genetic relationship of medicinal species in Dipsacus from China by SRAP.

    PubMed

    Chen, Da-xia; Zhang, Xue; Wang, Yu; Li, Long-yun; Zhang, Ze

    2015-07-01

    The author detected the genetic diversity and genetic relationship within and among eight medicinal species of Dipsacus by the approach of sequence-related amplified polymorphism (SRAP). The associated genetic parameters were calculated by POPGENE 1.31. The Genetic distance was calculated by TREECONW and the systematic diagrams of genetic relationship were clustered by UPG-MA. The results showed that, using 26 primers, a total of 558 bands were produced, of which 539 were polymorphic loci. There was a high level of genetic diversity among species (PPB = 96.59%, Na = 1.9659, Na = 1.3375, H = 0.2143, I = 0.3423). However, genetic diversity was lower within species, the average of genetic parameters was PPB = 6.97%, Na = 1.0697, Na = 1.0311, H = 0.0187, I = 0.0291. The Nei's genetic differentiation coefficient was 0.9126, indicated that most of the genetic variation existed among species. By clustering analysis, different individuals gathered in the same group and the classified result of SRAP marker between traditional modal characters was almost same. The results confirmed that SRAP marker can be used as one of the effective methods to reveal the genetic diversity and relationship among medicinal species of Dipsacus. PMID:26697678

  2. Ethnohistory, intertribal relationships, and genetic diversity among Amazonian Indians.

    PubMed

    Aguiar, G F

    1991-12-01

    The influence of recent ethnohistorical factors on the microevolution of South American Indians has not been adequately evaluated by population geneticists. This makes difficult a reasonable interpretation of the present genetic structure of these groups. In this article the genetic diversity of 18 tribes of the Amazon and neighboring areas belonging to 3 linguistic groups (Tupi, Carib, and Gê) is analyzed in light of documentary sources about historical events, such as demographic changes, geographic movements, intertribal relationships, and marriage practices, that have taken place since the end of the eighteenth century. The high depopulation rate suffered by the Tupi groups (61.4% on average) is a probable factor conditioning the large intergroup genetic distances in this linguistic stock, for depopulation is a phenomenon associated with random genetic drift caused by a bottleneck effect. On the other hand, the relatively high similarity of the Gê and the Carib shows an association with two main factors: (1) reduced spatial dispersion of the Gê in the recent past, providing adequate conditions for within-stock gene flow, and (2) strong tradition of intergroup contacts among the Carib, frequently followed by genetic admixture and even fusion of groups, as verified for the Wayana and the Aparaí. The patterns of biologic variation of some Tupi tribes (Waiãpi, Emerillon, Parakanã, and Assurini) are better explained by historical and regional contingencies than by linguistic classification. PMID:1959909

  3. 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 ...

  4. 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 results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

  5. Genetic diversity and genetic relationships in Hyacinthaceae in India using RAPD and SRAP markers.

    PubMed

    Jehan, Tabassum; Vashishtha, Amit; Yadav, S R; Lakhanpaul, Suman

    2014-01-01

    Genetic diversity and relationship among three genera namely Drimia, Dipcadi and Ledebouria of Hyacinthaceae in India was studied using RAPD and SRAP markers. Twenty one RAPD primers and nine SRAP were used for analyzing 41 accessions. RAPD gave an average 12.6 markers per primer, while SRAP generated 10.1 markers per primer pair. The family emerged very diverged with high polymorphism. The study resolved the three genera into monophyletic groups corresponding to three subfamilies; Urginoideae, Hyacinthoideae and Ornithogaloideae. Drimia wightii emerged a very distinct species and species specific markers were obtained with both marker systems. AMOVA analysis also revealed the genera to be quite well diverged. The two markers showed high correlation (r = 0.932) in Mantel matrix crresspondance test. The combined data also showed a very good correlation with the respective markers individually. PMID:24554844

  6. 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

    2014-01-01

    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. PMID:25299087

  7. 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.

  8. Evaluation of Lespedeza Germplasm Genetic Diversity and Its Phylogenetic Relationship with the Genus Kummerowia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago, cowpea and soybea...

  9. Genetic diversity and phylogenetic relationships among sugarcane and related species determined from microsatellite DNA data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and phylogenetic relationships were assessed among 105 clones of commercial sugarcane hybrids and related Saccharum species using 22 microsatellite (SSR) DNA markers. These included 17 sugarcane cultivars from the U.S. mainland, 23 S. officinarum clones, 16 S. robustum clones, 15 ...

  10. Genetic Diversity and Phylogenetic Relationships of the USDA Vigna Germplasm Collection Assessed by Gene-Derived Markers and Screening

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogenetic relationships in the USDA Vigna germplasm collection were unclear and their genetic diversity had not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 g...

  11. Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers.

    PubMed

    Korir, N K; Diao, W; Tao, R; Li, X; Kayesh, E; Li, A; Zhen, W; Wang, S

    2014-01-01

    The genetic diversity and relationship of 42 tomato varieties sourced from different geographic regions was examined with EST-SSR markers. The genetic diversity was between 0.18 and 0.77, with a mean of 0.49; the polymorphic information content ranged from 0.17 to 0.74, with a mean of 0.45. This indicates a fairly high degree of diversity among these tomato varieties. Based on the cluster analysis using unweighted pair-group method with arithmetic average (UPGMA), all the tomato varieties fell into 5 groups, with no obvious geographical distribution characteristics despite their diverse sources. The principal component analysis (PCA) supported the clustering result; however, relationships among varieties were more complex in the PCA scatterplot than in the UPGMA dendrogram. This information about the genetic relationships between these tomato lines helps distinguish these 42 varieties and will be useful for tomato variety breeding and selection. We confirm that the EST-SSR marker system is useful for studying genetic diversity among tomato varieties. The high degree of polymorphism and the large number of bands obtained per assay shows that SSR is the most informative marker system for tomato genotyping for purposes of rights/protection and for the tomato industry in general. It is recommended that these varieties be subjected to identification using an SSR-based manual cultivar identification diagram strategy or other easy-to-use and referable methods so as to provide a complete set of information concerning genetic relationships and a readily usable means of identifying these varieties. PMID:24446286

  12. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

    PubMed Central

    Egito, Andra A; Paiva, Samuel R; Albuquerque, Maria do Socorro M; Mariante, Arthur S; Almeida, Leonardo D; Castro, Silvia R; Grattapaglia, Dario

    2007-01-01

    Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine). For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The genetic data was able to shed light on a number of issues related to the local breeds origin and structure. The Brazilian Creole breeds are all important and viable targets for conservation for they display peculiar traits both phenotypic and of cultural and historical nature that deserve conservation efforts. PMID:18067665

  13. Dogrib Indians of the Northwest Territories, Canada: genetic diversity and genetic relationship among subarctic Indians.

    PubMed

    Szathmary, E J

    1983-01-01

    Phenotypes and gene frequencies of genes at the ABO, Rhesus, MNSs, Diego, Duffy, Kell, Kp, Kidd and P blood group systems are presented for three villages of Dogrib Indians. This population resides between Great Slave and Great Bear Lakes in the Northwest Territories of Canada. Until recently they pursued an exclusively hunting-gathering-fishing lifestyle in the subarctic forest. Maximum European admixture in the Dogrib is 8.7%. Nei's coefficient of gene diversity, GST is 0.0121. Blood group data from other Athapaskan-speaking Indians were also examined. GST for Kutchin villages is approximately 1.1%. GST obtained over five tribes of Northern Athapaskans is 0.0264, a figure slightly lower than that found in comparable groups of Mexican Indians. Overall genetic differentiation (HT) in Northern Athapaskans was greater than in the Mexicans, presumably because of high, though nonquantifiable European admixture in some of the tribes. The bulk of the genetic variability in Athapaskans exists within tribes, and then within villages of the same tribe. Genetic distance analysis with Nei's standard distance D shows that Dogrib and Kutchin Indians are very close. Geographic proximity has no significant influence on inter-tribal gene flow, but is significantly associated with intra-tribal gene flow. PMID:6838162

  14. Assessment of genetic diversity and relationships among caladium cultivars and species using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Caladium (Caladium hortulanum Birdsey) is an important aroid widely used in the ornamental plant industry. Concerns have been raised about possible loss of genetic diversity due to a drastic decline in the number of cultivars in the last century. This study assessed genetic diversity and relationshi...

  15. Geographic description of genetic diversity and genetic relationships in the USDA Rice World Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in ...

  16. The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community, Mexico

    PubMed Central

    Simental-Rodrguez, Sergio Leonel; Quiones-Prez, Carmen Zulema; Moya, Daniel; Hernndez-Tecles, Enrique; Lpez-Snchez, Carlos Antonio; Wehenkel, Christian

    2014-01-01

    Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martnez is an endemic species listed as Endangered on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities. PMID:25375134

  17. Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation.

    PubMed

    Lus, C; Juras, R; Oom, M M; Cothran, E G

    2007-02-01

    There are three native Portuguese horse breeds: Lusitano, Sorraia and Garrano. This study compares diversity patterns of 17 protein and 12 microsatellite markers in these three as well as 30 other breeds to infer relationships among the breeds and to compare levels of polymorphism of these breeds for use in conservation efforts. The Garrano and the Lusitano showed a high level of genetic diversity, similar to that observed for most of the other analysed breeds, while the Sorraia and Friesian breeds showed low levels of variation for both genetic marker types. The combined protein and microsatellite data produced a tree that fit historical records well and with greater confidence levels than those for either data set alone. The combined genetic diversity and relationship information provides important baseline data for future breed conservation efforts, especially for a critically endangered breed such as the Sorraia. PMID:17257184

  18. Genetic Diversity and Genetic Structure of Different Types of Natural Populations in Osmanthus fragrans Lour. and the Relationships with Sex Ratio, Population Structure, and Geographic Isolation

    PubMed Central

    Hu, Shaoqing; Wu, Shuai; Wang, Yiguang; Zhang, Yuanyan

    2014-01-01

    Osmanthus fragrans Lour., an evergreen small tree, has the rare sexual system of androdioecy (coexistence of males and hermaphrodites), once with wide-spread natural distribution in the areas of the South Yangzi river basin. However, due to excessive human utilization, natural distribution became fragmented and the number and size of natural populations reduced sharply. With four different types of natural populations from the same region as research object, we aim to provide a comparative analysis on the relationships among genetic diversity, sexual system, population structure and size, and geographic isolation by ISSR. In genetic parameters of Ne, He, and I, the LQGC population had the highest value and the LQZGQ population had the lowest value. These indicated that LQGC population showed the highest genetic diversity, followed by QDH and JN population, and LQZGQ population exhibited the lowest genetic diversity. Genetic diversity in populations is closely related to population structure, reproduction mode, and sex ratio. However, there seems to be no obvious correlation between genetic diversity and population size. The results of AMOVA showed that genetic variations mostly occurred within populations. It indicates that no significant genetic differentiation among populations occurs, and geographic isolation has no significant effect on genetic diversity. PMID:25436228

  19. Assessment of Genetic Diversity of Lespedeza Germplasm and Analysis of Its Phylogenetic Relationship with the Genus Kummerowia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence (EST-SSR) markers derived from Medicago, cowpea and soybean were used...

  20. Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP)

    PubMed Central

    Laurentin, Hernán E; Karlovsky, Petr

    2006-01-01

    Background Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP). Results Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied. Conclusion We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame. PMID:16483380

  1. Genetic diversities of 20 novel autosomal STRs in Chinese Xibe ethnic group and its genetic relationships with neighboring populations.

    PubMed

    Meng, Hao-Tian; Zhang, Li-Ping; Wu, Hua; Yang, Chun-Hua; Chen, Jian-Gang; Wang, Yan; Yan, Jiang-Wei; Wang, Hong-Dan; Zhang, Yu-Dang; Liu, Wen-Juan; Zhu, Bo-Feng

    2015-02-25

    In the present study, we investigated the genetic polymorphisms of 20 novel STR loci and one previously studied locus in the Xibe ethnic group from China, as well as its genetic relationships with neighboring populations. Totally 226 unrelated healthy Xibe individuals were involved in the study. At least 5 alleles were observed for each locus, with the minimum and maximum allelic frequencies of 0.0022 and 0.5221, respectively. We obtained the lowest and highest observed heterozygosity and expected heterozygosity at locus D1S1627 and D19S433, respectively. The values of combined power of discrimination and probability of exclusion of all the 21 STR loci were 0.99999999999999999997310 and 0.999998650, respectively. Analyses of interpopulation differentiation, principal component analysis, genetic distance and phylogenetic tree revealed the relationships between Xibe group and its neighboring groups, showing that the studied Xibe group had a close genetic relationship with the Mongolian group. The present results indicated that these 21 STR loci had high genetic polymorphisms in the studied Xibe group, and were capable for the paternity testing and individual identification in forensic application. PMID:25528265

  2. Relationships between Genetic Diversity and Fusarium Toxin Profiles of Winter Wheat Cultivars.

    PubMed

    Gral, Tomasz; Stuper-Szablewska, Kinga; Bu?ko, Maciej; Boczkowska, Maja; Walentyn-Gral, Dorota; Wi?niewska, Halina; Perkowski, Juliusz

    2015-09-01

    Fusarium head blight is one of the most important and most common diseases of winter wheat. In order to better understanding this disease and to assess the correlations between different factors, 30 cultivars of this cereal were evaluated in a two-year period. Fusarium head blight resistance was evaluated and the concentration of trichothecene mycotoxins was analysed. Grain samples originated from plants inoculated with Fusarium culmorum and naturally infected with Fusarium species. The genetic distance between the tested cultivars was determined and data were analysed using multivariate data analysis methods. Genetic dissimilarity of wheat cultivars ranged between 0.06 and 0.78. They were grouped into three distinct groups after cluster analysis of genetic distance. Wheat cultivars differed in resistance to spike and kernel infection and in resistance to spread of Fusarium within a spike (type II). Only B trichothecenes (deoxynivalenol, 3-acetyldeoxynivalenol and nivalenol) produced by F. culmorum in grain samples from inoculated plots were present. In control samples trichothecenes of groups A (H-2 toxin, T-2 toxin, T-2 tetraol, T-2 triol, scirpentriol, diacetoxyscirpenol) and B were detected. On the basis of Fusarium head blight assessment and analysis of trichothecene concentration in the grain relationships between morphological characters, Fusarium head blight resistance and mycotoxins in grain of wheat cultivars were examined. The results were used to create of matrices of distance between cultivars - for trichothecene concentration in inoculated and naturally infected grain as well as for FHB resistance Correlations between genetic distance versus resistance/mycotoxin profiles were calculated using the Mantel test. A highly significant correlation between genetic distance and mycotoxin distance was found for the samples inoculated with Fusarium culmorum. Significant but weak relationships were found between genetic distance matrix and FHB resistance or trichothecene concentration in naturally infected grain matrices. PMID:26361471

  3. Relationships between Genetic Diversity and Fusarium Toxin Profiles of Winter Wheat Cultivars

    PubMed Central

    Góral, Tomasz; Stuper-Szablewska, Kinga; Buśko, Maciej; Boczkowska, Maja; Walentyn-Góral, Dorota; Wiśniewska, Halina; Perkowski, Juliusz

    2015-01-01

    Fusarium head blight is one of the most important and most common diseases of winter wheat. In order to better understanding this disease and to assess the correlations between different factors, 30 cultivars of this cereal were evaluated in a two-year period. Fusarium head blight resistance was evaluated and the concentration of trichothecene mycotoxins was analysed. Grain samples originated from plants inoculated with Fusarium culmorum and naturally infected with Fusarium species. The genetic distance between the tested cultivars was determined and data were analysed using multivariate data analysis methods. Genetic dissimilarity of wheat cultivars ranged between 0.06 and 0.78. They were grouped into three distinct groups after cluster analysis of genetic distance. Wheat cultivars differed in resistance to spike and kernel infection and in resistance to spread of Fusarium within a spike (type II). Only B trichothecenes (deoxynivalenol, 3-acetyldeoxynivalenol and nivalenol) produced by F. culmorum in grain samples from inoculated plots were present. In control samples trichothecenes of groups A (H-2 toxin, T-2 toxin, T-2 tetraol, T-2 triol, scirpentriol, diacetoxyscirpenol) and B were detected. On the basis of Fusarium head blight assessment and analysis of trichothecene concentration in the grain relationships between morphological characters, Fusarium head blight resistance and mycotoxins in grain of wheat cultivars were examined. The results were used to create of matrices of distance between cultivars – for trichothecene concentration in inoculated and naturally infected grain as well as for FHB resistance Correlations between genetic distance versus resistance/mycotoxin profiles were calculated using the Mantel test. A highly significant correlation between genetic distance and mycotoxin distance was found for the samples inoculated with Fusarium culmorum. Significant but weak relationships were found between genetic distance matrix and FHB resistance or trichothecene concentration in naturally infected grain matrices. PMID:26361471

  4. Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers.

    PubMed

    Ben Tamarzizt, H; Ben Mustapha, S; Baraket, G; Abdallah, D; Salhi-Hannachi, A

    2015-01-01

    The usefulness of random amplified microsatellite polymorphism markers to study the genetic diversity and relationships among cultivars belonging to Prunus salicina and P. domestica and their wild relatives (P. insititia and P. spinosa) was investigated. A total of 226 of 234 bands were polymorphic (96.58%). The 226 random amplified microsatellite polymorphism markers were screened using 15 random amplified polymorphic DNA and inter-simple sequence repeat primers combinations for 54 Tunisian plum accessions. The percentage of polymorphic bands (96.58%), the resolving power of primers values (135.70), and the polymorphic information content demonstrated the efficiency of the primers used in this study. The genetic distances between accessions ranged from 0.18 to 0.79 with a mean of 0.24, suggesting a high level of genetic diversity at the intra- and interspecific levels. The unweighted pair group with arithmetic mean dendrogram and principal component analysis discriminated cultivars efficiently and illustrated relationships and divergence between spontaneous, locally cultivated, and introduced plum types. These procedures showed continuous variation that occurs independently of the status of the species and geographical origin of the plums. In this study, random amplified microsatellite polymorphism was found to be as a reliable molecular marker for fingerprinting and for examining the diversity study of the plum and its relatives. PMID:25867340

  5. Soybean Molecular Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A history of the various DNA marker types used in the assessment of molecular genetic diversity in soybean [Glycine max (L.) Merr.] is followed by a description of a number of studies on the assessment of genetic diversity. These studies include a review of reports on 1) the quantification and comp...

  6. Genetic diversity and evolutionary relationships among Legionella pneumophila clinical isolates, Portugal, 1987 to 2012.

    PubMed

    Chasqueira, M J; Rodrigues, L; Nascimento, M; Ramos, M; Marques, T

    2014-01-01

    The genetic diversity of 89 clinical Legionella isolates, collected between 1987 and 2012, in 22 hospitals from the five regions of Portugal, was analysed in this study using monoclonal antibodies (MAbs) of the Dresden panel and the sequence-based typing (SBT) protocol. The eBURST algorithm was used to infer levels of relatedness between isolates. All isolates collected were Legionella pneumophila, which were further characterised into four subgroups by MAbs, and 30 sequence types (STs) by SBT. Twelve of the STs were unique to Portugal; one of them (ST100) was represented by 32 epidemiologically related isolates. The ST44 was the profile with the highest number of epidemiologically unrelated isolates. The eBURST analyses indicate that, within the group formed by the 30 STs identified in this study, 17 STs were genetically close to at least another ST in the group. The comparison between the eBURST diagrams obtained with the STs from this study and the entire SBT database of the European Working Group for Legionella, showed that 24 (seven of them unique to Portugal) of our 30 STs were related with STs identified in others countries. These results suggest that the population of L. pneumophila clinical strains in Portugal includes both worldwide and local strains. PMID:25425515

  7. [Genetic diversity and relationships of northern eurasia populations for polymorphic Alu-insertions].

    PubMed

    Khitrinskaia, I Iu; Khar'kov, V N; Voevoda, M I; Stepanova, V A

    2014-01-01

    We for the first time have examined the autosomal gene pool of the Siberia, Central Asian and the Far East populations (27 populations of 12 ethnic groups) using a set of polymorphic Alu insertions in the human genome. The results of the analysis testify (i) to a significant level of genetic diversity in the Northern Eurasian populations and (ii) to a considerable differentiation of gene pool in the population of this region. It has been shown that at the CD4 locus, the frequency of Alu (-) is inversely related to the Mongoloid component of the population, the lowest and highest frequencies of the Alu deletion at locus CD4 were recorded respectively in Eskimo (0.012) and Russian and Ukrainian (0.35). The analysis of gene flow proved Caucasoid populations (Russian, Tajik and Uzbek), as well as those of Turkic ethnic groups from the Southern Siberia (Altaians and Tuvinians) and Khanty and Mansy populations to be the recipients of a considerable gene flow from the outside of the concerned population system, as compared with the East Siberian and the Far East ethnic groups. The results of the correlation analysis received with use polymorphic Alu insertion testify to the greatest correlation of genetic distances with anthropological characteristics of populations. PMID:25842827

  8. Artificial selection with traditional or genomic relationships: consequences in coancestry and genetic diversity

    PubMed Central

    Rodrguez-Ramilo, Silvia Teresa; Garca-Corts, Luis Alberto; de Cara, Mara ngeles Rodrguez

    2015-01-01

    Estimated breeding values (EBVs) are traditionally obtained from pedigree information. However, EBVs from high-density genotypes can have higher accuracy than EBVs from pedigree information. At the same time, it has been shown that EBVs from genomic data lead to lower increases in inbreeding compared with traditional selection based on genealogies. Here we evaluate the performance with BLUP selection based on genealogical coancestry with three different genome-based coancestry estimates: (1) an estimate based on shared segments of homozygosity, (2) an approach based on SNP-by-SNP count corrected by allelic frequencies, and (3) the identity by state methodology. We evaluate the effect of different population sizes, different number of genomic markers, and several heritability values for a quantitative trait. The performance of the different measures of coancestry in BLUP is evaluated in the true breeding values after truncation selection and also in terms of coancestry and diversity maintained. Accordingly, cross-performances were also carried out, that is, how prediction based on genealogical records impacts the three other measures of coancestry and inbreeding, and viceversa. Our results show that the genetic gains are very similar for all four coancestries, but the genomic-based methods are superior to using genealogical coancestries in terms of maintaining diversity measured as observed heterozygosity. Furthermore, the measure of coancestry based on shared segments of the genome seems to provide slightly better results on some scenarios, and the increase in inbreeding and loss in diversity is only slightly larger than the other genomic selection methods in those scenarios. Our results shed light on genomic selection vs. traditional genealogical-based BLUP and make the case to manage the population variability using genomic information to preserve the future success of selection programmes. PMID:25904933

  9. Genetic diversity and relationships in cultivars of Lolium multiflorum Lam. using sequence-related amplified polymorphism markers.

    PubMed

    Huang, L K; Jiang, X Y; Huang, Q T; Xiao, Y F; Chen, Z H; Zhang, X Q; Miao, J M; Yan, H D

    2014-01-01

    Sequence-related amplified polymorphism (SRAP) markers were used to analyze and estimate the genetic variability, level of diversity, and relationships among 20 cultivars and strains of annual ryegrass (Lolium multiflorum Lam.). Eighteen SRAP primer combinations generated 334 amplification bands, of which 298 were polymorphic. The polymorphism information content ranged from 0.4715 (me10 + em1) to 0.5000 (me5 + em7), with an average of 0.4921. The genetic similarity coefficient ranged from 0.4304 to 0.8529, and coefficients between 0.65 and 0.90 accounted for 90.00%. The cluster analysis separated the accessions into five groups partly according to their germplasm resource origins. PMID:25501225

  10. REGION-WIDE GENETIC STRUCTURE OF THE CENTRAL STONEROLLER (CAMPOSTOMA ANOMALUM) AND THE RELATIONSHIP OF GENETIC DIVERSITY TO ENVIRONMENTAL QUALITY

    EPA Science Inventory

    Anthropogenic stressors that reduce population size, alter migration corridors or modify mutational and selective forces on populations are expected to leave a lasting genetic footprint on the distribution of intraspecific genetic variation. Thus, the pattern of intraspecific gen...

  11. GENETIC DIVERSITY IN HYDRANGEA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Since the extensive study by McClintock in 1957, few systematic studies have been devoted to Hydrangea, a woody genus containing ~26 species. A detailed understanding of the genus would enable breeding programs to explore the genetic diversity found in wild species....

  12. Imposing genetic diversity.

    PubMed

    Sparrow, Robert

    2015-01-01

    The idea that a world in which everyone was born "perfect" would be a world in which something valuable was missing often comes up in debates about the ethics of technologies of prenatal testing and preimplantation genetic diagnosis (PGD). This thought plays an important role in the "disability critique" of prenatal testing. However, the idea that human genetic variation is an important good with significant benefits for society at large is also embraced by a wide range of figures writing in the bioethics literature, including some who are notoriously hostile to the idea that we should not select against disability. By developing a number of thought experiments wherein we are to contemplate increasing genetic diversity from a lower baseline in order to secure this value, I argue that this powerful intuition is more problematic than is generally recognized, especially where the price of diversity is the well-being of particular individuals. PMID:26030484

  13. Close genetic relationships in vast territories: autosomal and X chromosome Alu diversity in Yakuts from Siberia.

    PubMed

    Rocan-Arj, Ares; Rodrguez-Botigu, Laura; Esteban, Esther; Theves, Catherine; Evdokimova, Larissa E; Fedorova, Sardana A; Gibert, Morgane; Crubezy, Eric; Moral, Pedro

    2013-01-01

    Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations. PMID:24466640

  14. Genetic diversity and relationships assessed by SSRs in the USDA Rice Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding a germplasm collection is essential for mining special genes and further development of the collection. The USDA rice (Oryza sativa L.) collection contains about 20,000 accessions from 116 countries. These diverse originations indicate a variety of different edaphic and climatic enviro...

  15. Genetic diversity and phylogenetic relationship in AA Oryza species as revealed by Rim2/Hipa CACTA transposon display.

    PubMed

    Kwon, Soon-Jae; Lee, Ju Kyong; Hong, Sung-Won; Park, Yong-Jin; McNally, Kenneth L; Kim, Nam-Soo

    2006-04-01

    CACTA is a class 2 transposon, that is very abundantly present in plant genomes. Using Rim2/Hipa CACTA transposon display (hereafter Rim2/Hipa-TD), we analyzed several A-genome diploid Oryza species that have a high distribution of the CACTA motifs. High levels of polymorphism were detected within and between the Oryza species. The African taxa, O. glaberrima and O. barthii, both showed lower levels of polymorphism than the Asian taxa, O. sativa, O. rufipogon, and O. nivara. However, O. longistaminata, another African taxon, showed levels of polymorphism that were similar to the Asian taxa. The Latin American taxon, O. glumaepatula, and the Australian taxon, O. meridionalis, exhibited intermediate levels of polymorphism between those of the Asian and African taxa. The lowest level of polymorphism was observed in O. glaberrima (32.1%) and the highest level of polymorphism was observed in O. rufipogon (95.7%). The phylogenetic tree revealed three major groups at the genetic similarity level of 0.409. The first group consisted of three Asian taxa, O. sativa, O. rufipogon and O. nivara. The second group consisted of three African taxa, O. glaberrima, O. barthii, O. longistaminata, and an American taxon, O. glumaepatula. The third group contained an Australian taxon, O. meridionalis. The clustering patterns of these species matched well with their geographical origins. Rim2/Hipa-TD appears to be a useful marker system for studying the genetic diversity and species relationships among the AA diploid Oryza species. PMID:16755133

  16. 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...

  17. Relationship between species diversity and ecotope diversity.

    PubMed

    Yue, Tian-Xiang; Li, Qi-Quan

    2010-05-01

    The relationship between species diversity and ecotope diversity has long been debated. But these debates seem meaningless because most of them were based on different definitions. In this paper, diversity has two components: richness based on the total number and evenness based on the relative abundance. Species diversity is distinguished into individual-counting diversity and biomass-based diversity. Ecotope diversity is divided into individual ecotope-counting diversity and ecotope-area based diversity. Under this definition, we make a comprehensive investigation into Dongzhi tableland of Loess Plateau by cooperating with local technicians. We find that individual-counting diversity is significantly correlated with biomass-based diversity in grassland ecosystems; individual ecotope-counting diversity and ecotope-area based diversity have a significant correlation. Therefore, it is unnecessary to divide species diversity into individual-counting diversity and biomass-based diversity in grassland ecosystems and to distinguish ecotope diversity into individual ecotope-counting and ecotope-area based diversity for the issues that have no special requirement for accuracy. But the analyses of the investigation data demonstrate that species diversity has no significant correlation with ecotope diversity. PMID:20586772

  18. 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

  19. Genetic Diversity and Societally Important Disparities.

    PubMed

    Rosenberg, Noah A; Kang, Jonathan T L

    2015-09-01

    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

  20. Molecular Epidemiology of Novel Pathogen "Brachyspira hampsonii" Reveals Relationships between Diverse Genetic Groups, Regions, Host Species, and Other Pathogenic and Commensal Brachyspira Species.

    PubMed

    Mirajkar, Nandita S; Bekele, Aschalew Z; Chander, Yogesh Y; Gebhart, Connie J

    2015-09-01

    Outbreaks of bloody diarrhea in swine herds in the late 2000s signaled the reemergence of an economically significant disease, swine dysentery, in the United States. Investigations confirmed the emergence of a novel spirochete in swine, provisionally designated "Brachyspira hampsonii," with two genetically distinct clades. Although it has since been detected in swine and migratory birds in Europe and North America, little is known about its genetic diversity or its relationships with other Brachyspira species. This study characterizes B. hampsonii using a newly developed multilocus sequence typing (MLST) approach and elucidates the diversity, distribution, population structure, and genetic relationships of this pathogen from diverse epidemiological sources globally. Genetic characterization of 81 B. hampsonii isolates, originating from six countries, with our newly established MLST scheme identified a total of 20 sequence types (STs) belonging to three clonal complexes (CCs). B. hampsonii showed a heterogeneous population structure with evidence of microevolution locally in swine production systems, while its clustering patterns showed associations with its epidemiological origins (country, swine production system, and host species). The close genetic relatedness of B. hampsonii isolates from different countries and host species highlights the importance of strict biosecurity control measures. A comparative analysis of 430 isolates representing seven Brachyspira species (pathogens and commensals) from 19 countries and 10 host species depicted clustering by microbial species. It revealed the close genetic relatedness of B. hampsonii with commensal Brachyspira species and also provided support for the two clades of B. hampsonii to be considered a single species. PMID:26135863

  1. Genetic diversity and relationship of Hedychium from Northeast India as dissected using PCA analysis and hierarchical clustering

    PubMed Central

    Basak, Supriyo; Ramesh, Aadi Moolam; Kesari, Vigya; Parida, Ajay; Mitra, Sudip; Rangan, Latha

    2014-01-01

    Molecular genetic fingerprints of eleven Hedychium species from Northeast India were developed using PCR based markers. Fifteen inter-simple sequence repeats (ISSRs) and five amplified fragment length polymorphism (AFLP) primers produced 547 polymorphic fragments. Positive correlation (r=0.46) was observed between the mean genetic similarity and genetic diversity parameters at the inter-species level. AFLP and ISSR markers were able to group the species according to its altitude and intensity of flower aroma. Cophenetic correlation coefficients between the dendrogram and the original similarity matrix were significant for ISSR (r=0.89) compared to AFLP (r=0.83) markers. This genetic characterization of Hedychium from Northeast India contributes to the knowledge of genetic structure of the species and can be used to define strategies for their conservation and management. PMID:25606430

  2. 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...

  3. 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

  4. Genetic diversity of Lycoris endemic to Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extensive taxonomic relationships among Lycoris Herb. (Amaryllidaceae) taxa native to Korea have not been analyzed previously. This study was carried out to investigate the hybrid origin, genetic diversity, and relationships of Lycoris taxa (L. flavescens, L. uydoensis, L. chejuensis, L. chinensis ...

  5. Genetic diversity, structure, gene flow and evolutionary relationships within the Sorghum bicolor wild-weedy-crop complex in a western African region.

    PubMed

    Sagnard, Fabrice; Deu, Monique; Dembl, Dkoro; Leblois, Raphal; Tour, Lassana; Diakit, Mohamed; Calatayud, Caroline; Vaksmann, Michel; Bouchet, Sophie; Mall, Yaya; Togola, Sabine; Traor, Pierre C Sibiry

    2011-11-01

    Gene flow between domesticated plants and their wild relatives is one of the major evolutionary processes acting to shape their structure of genetic diversity. Earlier literature, in the 1970s, reported on the interfertility and the sympatry of wild, weedy and cultivated sorghum belonging to the species Sorghum bicolor in most regions of sub-Saharan Africa. However, only a few recent surveys have addressed the geographical and ecological distribution of sorghum wild relatives and their genetic structure. These features are poorly documented, especially in western Africa, a centre of diversity for this crop. We report here on an exhaustive in situ collection of wild, weedy and cultivated sorghum assembled in Mali and in Guinea. The extent and pattern of genetic diversity were assessed with 15 SSRs within the cultivated pool (455 accessions), the wild pool (91 wild and weedy forms) and between them. F (ST) and R (ST) statistics, distance-based trees, Bayesian clustering methods, as well as isolation by distance models, were used to infer evolutionary relationships within the wild-weedy-crop complex. Firstly, our analyses highlighted a strong racial structure of genetic diversity within cultivated sorghum (F (ST) = 0.40). Secondly, clustering analyses highlighted the introgressed nature of most of the wild and weedy sorghum and grouped them into two eco-geographical groups. Such closeness between wild and crop sorghum could be the result of both sorghum's domestication history and preferential post-domestication crop-to-wild gene flow enhanced by farmers' practices. Finally, isolation by distance analyses showed strong spatial genetic structure within each pool, due to spatially limited dispersal, and suggested consequent gene flow between the wild and the crop pools, also supported by R (ST) analyses. Our findings thus revealed important features for the collection, conservation and biosafety of domesticated and wild sorghum in their centre of diversity. PMID:21811819

  6. Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.

    PubMed

    Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

    2015-01-01

    Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin. PMID:25730081

  7. 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,

  8. Genetic Diversity of Toscana Virus

    PubMed Central

    Collao, Ximena; Palacios, Gustavo; Sanbonmatsu-Gmez, Sara; Prez-Ruiz, Mercedes; Negredo, Ana I.; Navarro-Mar, Jos-Mara; Grandadam, Marc; Aransay, Ana Maria; Lipkin, W. Ian; Tenorio, Antonio

    2009-01-01

    Distribution of Toscana virus (TOSV) is evolving with climate change, and pathogenicity may be higher in nonexposed populations outside areas of current prevalence (Mediterranean Basin). To characterize genetic diversity of TOSV, we determined the coding sequences of isolates from Spain and France. TOSV is more diverse than other well-studied phleboviruses (e.g.,Rift Valley fever virus). PMID:19331735

  9. 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,…

  10. At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

    PubMed Central

    Rowold, Diane; Garcia-Bertrand, Ralph; Calderon, Silvia; Rivera, Luis; Benedico, David Perez; Alfonso Sanchez, Miguel A.; Chennakrishnaiah, Shilpa; Varela, Mangela; Herrera, Rene J.

    2014-01-01

    Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific. PMID:25606451

  11. At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes.

    PubMed

    Rowold, Diane; Garcia-Bertrand, Ralph; Calderon, Silvia; Rivera, Luis; Benedico, David Perez; Alfonso Sanchez, Miguel A; Chennakrishnaiah, Shilpa; Varela, Mangela; Herrera, Rene J

    2014-12-01

    Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific. PMID:25606451

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

    PubMed Central

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

    2015-01-01

    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. PMID:25674097

  13. Genetic diversity and relationships among Chinese Eucommia ulmoides cultivars revealed by sequence-related amplified polymorphism, amplified fragment length polymorphism, and inter-simple sequence repeat markers.

    PubMed

    Li, Y; Wang, S H; Li, Z Q; Jin, C F; Liu, M H

    2014-01-01

    Sequence-related amplified polymorphism (SRAP), amplified fragment length polymorphism (AFLP), and inter-simple sequence repeat (ISSR) markers were used to estimate the genetic diversity and relationships among Eucommia ulmoides cultivars in China. A total of 240, 192, and 150 DNA fragments were detected by 10 SRAP primer combinations, 10 AFLP primer combinations, and 10 ISSR primers, among which 89.2, 65.1, and 88.0% of the fragments were polymorphic, respectively. Cluster analysis revealed that Qinzhong No. 3, Xiaoyeci, Qinzhong No. 1, and Qinzhong No. 2 formed independent clusters. The other 15 cultivars exhibited two clusters. The results of this study will help in the selection of parents for both genome mapping and crossbreeding purposes. PMID:25366761

  14. 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

  15. Genetic Diversity Increases Insect Herbivory on Oak Saplings

    PubMed Central

    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. PMID:22937168

  16. Genetic diversity and phylogenetic relationships between birches and alders using ITS, 18S rRNA and rbcL gene sequences.

    PubMed

    Savard, L; Michaud, M; Bousquet, J

    1993-06-01

    The Betuleae is one of the two Betulaceae tribes and contains two genera, the actinorhizal genus Alnus and the nonactinorhizal genus Betula. To elucidate the phylogenetic relationships within the tribe and compare the relative amounts of genetic diversity between the genera Alnus and Betula, rbcL and 18S rRNA gene sequences as well as rDNA internal transcribed spacer (ITS1 and ITS2) sequences were obtained and compared. In rbcL and 18S rRNA, several substitutions were detected between Alnus and Betula but no variation was observed within Alnus. Minimal length variation was observed among ITS sequences. The numbers of substitutions per site for ITS were, on average, close to 10 times those estimated for 18S between Alnus and Betula. In ITS, numbers of substitutions were, on average, more than twice as large between genera than within genera. Phylogenies from ITS sequences were estimated using neighbor-joining analysis of substitution rates, maximum likelihood and parsimony methods. Each of the two genera appeared monophyletic, which was supported by high bootstrap estimates. Relationships among the three sections of Betula analyzed were also better resolved than those among the three subgenera of Alnus analyzed. Phylogenies estimated from ITS sequences suggested a relatively recent diversification of each genus, in agreement with fossil data. PMID:8025718

  17. Hidden relationships and genetic diversity: Molecular phylogeny and phylogeography of the Levantine lizards of the genus Phoenicolacerta (Squamata: Lacertidae).

    PubMed

    Tamar, Karin; Carranza, Salvador; In den Bosch, Herman; Sindaco, Roberto; Moravec, Ji?; Meiri, Shai

    2015-10-01

    The Levant region witnessed dramatic tectonic events and climatic fluctuations that changed the historical landscape of the area and consequently influenced the cladogenesis and distribution of the local biota. In this study we use information from two mitochondrial and two nuclear genes and species delimitation methods in order to obtain the first robust time-calibrated molecular phylogeny of the Levantine rock lizards of the genus Phoenicolacerta. We sampled from across its distributional range with the aim to clarify its systematics, biogeography and evolution. Our results suggest that the genus includes two well-supported clades, one comprising solely the montane species Phoenicolacerta kulzeri, and the other including the three remaining species, the relatively widespread, P. laevis, the Syrian-Turkish P. cyanisparsa and the Cypriot endemic P. troodica. We found that both P. laevis and P. cyanisparsa are not monophyletic, as the Turkish populations of P. laevis branch within P. cyanisparsa. We found high levels of undescribed diversity within P. laevis which necessitate a thorough revision. We suggest that Phoenicolacerta started radiating during the mid-late Miocene, and that both vicariance and dispersal events shaped the diversification and distribution of the genus concomitantly with the formation of major geological structures and climatic fluctuations in the Levant. These results highlight the region as an important center of speciation, contributing to the species diversity of the eastern Mediterranean. PMID:25987529

  18. Genetic diversity of the Arctic fox using SRAP markers.

    PubMed

    Zhang, M; Bai, X J

    2013-01-01

    Sequence-related amplified polymorphism (SRAP) is a recently developed molecular marker technique that is stable, simple, reliable, and achieves moderate to high numbers of codominant markers. This study is the first to apply SRAP markers in a mammal, namely the Arctic fox. In order to investigate the genetic diversity of the Arctic fox and to provide a reference for use of its germplasm, we analyzed 7 populations of Arctic fox by SRAP. The genetic similarity coefficient, genetic distance, proportion of polymorphic loci, total genetic diversity (Ht), genetic diversity within populations (Hs), and genetic differentiation (Gst) were calculated using the Popgene software package. The results indicated abundant genetic diversity among the different populations of Arctic fox studied in China. The genetic similarity coefficient ranged from 0.1694 to 0.0417, genetic distance ranged from 0.8442 to 0.9592, and the proportion of polymorphic loci was smallest in the TS group. Genetic diversity ranged from 0.2535 to 0.3791, Ht was 0.3770, Hs was 0.3158, Gst was 0.1624, and gene flow (Nm) was estimated at 2.5790. Thus, a high level of genetic diversity and many genetic relationships were found in the populations of Arctic fox evaluated in this study. PMID:24338412

  19. Relationship of Injection Drug Use, Antiretroviral Therapy Resistance, and Genetic Diversity in the HIV-1 pol Gene

    PubMed Central

    Kowalski, Jeanne; Gange, Stephen J.; Schneider, Michael F.; Tsai, Hua-Ling; Templeton, Alan; Shao, Qiujia; Zhang, Guang Wen; Yeh, Mei-Fen; Young, Mary; Markham, Richard B.

    2010-01-01

    Objectives To determine if a history of injection drug use influences genotypic PI resistance to antiretroviral agents.. Methods We assessed the presence of resistance mutations in PI-naive injection drug users (IDUs) and non-IDUs participating in the Womens Interagency HIV Study. Eighteen HIV-infected participants who reported injection drug use prior to study enrollment and 32 HIV-infected non-IDUs contributed a total of 34 and 65 person-visits, respectively to analyses. Results Based on data from multiple clones obtained from different time points from each individual we determined that primary PI resistance mutations were more frequent among person-visits contributed by IDUs (24%) than non-IDUs (8%, p=0.05). While neither reached statistical significance, diversity was higher within the protease region among study visits carrying PI resistant clones at both the nucleotide level (2.66 vs. 2.35; p=0.08) and at the amino acid level (1.60 vs. 1.32; p=0.23). Most of the primary resistance mutations could not be detected using the standard population sequencing employed in the clinical setting. Five of six individuals in whom clones encoding PI resistance mutations were identified failed PI-containing HAART within 12 months of therapy initiation. Conclusions Our findings indicate that more aggressive sampling for resistance mutations among viral clones prior to HAART initiation might permit selection of more effective treatment, particularly in IDUs. PMID:19214121

  20. Genetic diversity in the red yeast Cryptococcus hungaricus and its phylogenetic relationship to some related basidiomycetous yeasts.

    PubMed

    Gcser, A; Hamari, Z; Pfeiffer, I; Varga, J; Kevei, F; Kucsera, J

    2001-12-01

    Cryptococcus hungaricus is a basidiomycetous yeast with the abilities to synthesize carotenoid pigments and to grow under psychrophile conditions. Six C. hungaricus strains have been isolated so far from different habitats. In this study we wished to clarify the relationships amongst them. Morphological and physiological characters, mitochondrial DNA restriction profiles, and the presence of mycoviruses were examined. Internal transcribed spacers together with the 5.8S rDNA, the D1/D2 region of 26S rDNA, and partial sequences of the 18S rRNA gene were also analysed. On the basis of the phylogenetic analyses the type strain CBS 4214(T) together with four other C. hungaricus isolates were closely related to Bullera armeniaca and Bullera crocea, while strain CBS 6569 was much more similar to Cystofilobasidium than to the other C. hungaricus isolates. PMID:12702346

  1. Diversity Maintenance in Genetic Programming

    NASA Astrophysics Data System (ADS)

    Motoki, Tatsuya; Numaguchi, Yasushi

    This paper is motivated by an experimental result that better performing genetic programming runs tend to have higher phenotypic diversity. To maintain phenotypic diversity, we apply implicit fitness sharing and its variant, called unfitness multiplying. To apply these methods to problems in which individuals have infinite kinds of possible behaviours, we classify posible behaviours into 50 achievement levels, and assign a reward or a penalty to each level. In implicit fitness sharing a reward is shared out among individuals with the same achievement level, and in unfitness multiplying a penalty is multiplied by the number of individuals with the same level and is distributed to related individuals. Five benchmark problems (11-multiplexer, sextic polynomial, four-sine, intertwined spiral, and artificial ant problems) are used to illustrate the effect of the methods. The results show that our methods clearly promote diversity and lead population to a smooth frequency distribution of achievement levels, and that our methods usually perform better than the original implicit fitness sharing on success rate and the best (raw) fitness. We also observe that the unfitness multiplying makes a quite different ranking over individuals than the one by the implicit fitness sharing.

  2. AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

    PubMed

    Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

    2016-04-01

    Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs. PMID:26762294

  3. 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...

  4. The relic Criollo cacao in Belize- genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cacao (Theobroma cacao L.) is native to the South American rainforest but it was domesticated in Mesoamerica. The relic Criollo cocoa in Belize has been well known in the premium chocolate market for its high-quality. Knowledge of genetic diversity in this variety is essential for efficient conserva...

  5. Personalized medicine and human genetic diversity.

    PubMed

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

    2014-09-01

    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

  6. Diversity of potato genetic resources.

    PubMed

    Machida-Hirano, Ryoko

    2015-03-01

    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

  7. 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

  8. 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...

  9. Genetic diversity, parasite prevalence and immunity in wild bumblebees

    PubMed Central

    Whitehorn, Penelope R.; Tinsley, Matthew C.; Brown, Mark J. F.; Darvill, Ben; Goulson, Dave

    2011-01-01

    Inbreeding and a consequent loss of genetic diversity threaten small, isolated populations. One mechanism by which genetically impoverished populations may become extinct is through decreased immunocompetence and higher susceptibility to parasites. Here, we investigate the relationship between immunity and inbreeding in bumblebees, using Hebridean island populations of Bombus muscorum. We sampled nine populations and recorded parasite prevalence and measured two aspects of immunity: the encapsulation response and levels of phenoloxidase (PO). We found that prevalence of the gut parasite Crithidia bombi was higher in populations with lower genetic diversity. Neither measure of immune activity was correlated with genetic diversity. However, levels of PO declined with age and were also negatively correlated with parasite abundance. Our results suggest that as insect populations lose heterozygosity, the impact of parasitism will increase, pushing threatened populations closer to extinction. PMID:20926436

  10. Genetic diversity, parasite prevalence and immunity in wild bumblebees.

    PubMed

    Whitehorn, Penelope R; Tinsley, Matthew C; Brown, Mark J F; Darvill, Ben; Goulson, Dave

    2011-04-22

    Inbreeding and a consequent loss of genetic diversity threaten small, isolated populations. One mechanism by which genetically impoverished populations may become extinct is through decreased immunocompetence and higher susceptibility to parasites. Here, we investigate the relationship between immunity and inbreeding in bumblebees, using Hebridean island populations of Bombus muscorum. We sampled nine populations and recorded parasite prevalence and measured two aspects of immunity: the encapsulation response and levels of phenoloxidase (PO). We found that prevalence of the gut parasite Crithidia bombi was higher in populations with lower genetic diversity. Neither measure of immune activity was correlated with genetic diversity. However, levels of PO declined with age and were also negatively correlated with parasite abundance. Our results suggest that as insect populations lose heterozygosity, the impact of parasitism will increase, pushing threatened populations closer to extinction. PMID:20926436

  11. Genetic selection and preservation of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For 100’s 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 risen and fallen out of favor o...

  12. Bovine Genetic Diversity Revealed By mtDNA Sequence Variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondrial DNA single nucleotide polymorphism (SNP) data were used to determine genetic distance, nucleotide diversity, construction of haplotypes, estimation of information contents, and phylogenic relationships in bovine HapMap breeds. The Bovine International HapMap panel consists of 720 anima...

  13. 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. PMID:26839689

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

    PubMed

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

    2015-08-01

    The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes. PMID:26188469

  15. 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

  16. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers.

    PubMed

    Ramakrishnan, M; Antony Ceasar, S; Duraipandiyan, V; Al-Dhabi, N A; Ignacimuthu, S

    2016-01-01

    We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60-70% GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6% polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard's similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94% per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100% homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard's similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4%; among populations it was 3% and within populations it was 93%. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions. PMID:26900542

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

    PubMed Central

    Gill-Langarica, Homar R.; Muruaga-Martnez, Jos S.; Vargas-Vzquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Prez, Netzahualcoyotl

    2011-01-01

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

  18. Diversity and Relationships of Eggplants from Three Geographically Distant Secondary Centers of Diversity

    PubMed Central

    Hurtado, Maria; Vilanova, Santiago; Plazas, Mariola; Gramazio, Pietro; Fonseka, H. Hemal; Fonseka, Ramya; Prohens, Jaime

    2012-01-01

    Eggplant (Solanum melongena L.) was domesticated in the Indo-Birmanian region, which is also the primary center of diversity for this crop. From there eggplant spread to other regions, and diversity accumulated in several secondary centers of diversity. We have assessed the diversity and relationships of 52 accessions of eggplant from three geographically distant secondary centers of diversity (China, Spain, and Sri Lanka) using 28 morphological descriptors and 12 highly polymorphic genomic SSRs. A wide variation was found for most morphological traits, and significant differences among the three centers of diversity were detected for 22 of these traits. The PCA analysis showed that eggplants from the three origins were morphologically differentiated, and accessions from each of the three secondary centers of diversity presented a typical combination of morphological characteristics. In this respect, discriminant analysis showed that accessions could be correctly classified to their origin using only six traits. The SSR characterization identified 110 alleles and allowed obtaining a unique genetic fingerprint for each accession. Many alleles were found to be private to each origin, but no universal alleles were found for any of the origins. The PCA analysis showed that the genetic differentiation among origins was less clear than for morphological traits, although the analysis of the population structure shows that accessions mostly group according to the origin, but also provides evidence of migration among the three secondary centers of diversity. The genetic diversity (HT) within each origin was high, ranging between HT = 0.5400 (Sri Lanka) and HT = 0.4943 (China), while the standardized genetic differentiation (G’ST) among origins was moderate (G’ST = 0.2657). The correlation between morphological and SSR distances was non-significant (r = 0.044), indicating that both data are complementary for the conservation of germplasm and breeding of eggplant. These results are relevant for the management of genetic resources, breeding programmes, and evolutionary studies of eggplant. PMID:22848589

  19. 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...

  20. Genetic Diversity in Pollen Abiotic Stress Tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in reproductive abiotic stress tolerance has been investigated by cotton breeders throughout the public and private sectors. The primary focus of these studies has been the evaluation of abiotic stress responses during the development of the flower prior to anthesis. Sterility in...

  1. Genetic diversity in pollen abiotic stress tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in reproductive abiotic stress tolerance has been investigated by cotton breeders throughout the public and private sectors. The primary focus of these studies has been the evaluation of abiotic stress responses during the development of the flower prior to anthesis. Sterility in...

  2. Cryptic genetic diversity in Dientamoeba fragilis.

    PubMed

    Johnson, J A; Clark, C G

    2000-12-01

    Uncertainty surrounding the role of Dientamoeba fragilis in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take D. fragilis diversity into account. PMID:11101615

  3. Cryptic Genetic Diversity in Dientamoeba fragilis

    PubMed Central

    Johnson, Jeanette A.; Clark, C. Graham

    2000-01-01

    Uncertainty surrounding the role of Dientamoeba fragilis in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take D. fragilis diversity into account. PMID:11101615

  4. 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...

  5. Does Genetic Diversity Predict Health in Humans?

    PubMed Central

    Lie, Hanne C.; Simmons, Leigh W.; Rhodes, Gillian

    2009-01-01

    Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC), has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d2) at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d2) at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations. PMID:19633717

  6. Phylogenetic relationships, recombination analysis, and genetic variability among diverse variants of tomato yellow leaf curl virus in Iran and the Arabian Peninsula: further support for a TYLCV center of diversity.

    PubMed

    Hosseinzadeh, Mohammad Reza; Shams-Bakhsh, Masoud; Osaloo, Shahrokh Kazempour; Brown, Judith K

    2014-03-01

    The discovery of five strains of TYLCV in Iran, including the most well-known and widespread, TYLCV-IL, spurred a detailed study of the full-length genomes of additional TYLCV field isolates and an in-depth analysis of phylogenetic relationships, extent of recombination, and genetic variability of TYLCV isolates within Iran and throughout the Arabian Peninsula. Phylogenetic analysis of complete genome sequences of TYLCV isolates from Iran and other countries revealed four monophyletic clusters could be differentiated based on geographical origin, indicating that recent dispersal of these populations (by the vector or by humans) from these four regions has occurred minimally, or not at all. Genetic analysis revealed that TYLCV-IL isolates from southern Iran possessed greater genetic variability than the northeastern isolates, a pattern that may be reflective of evolution driven by geographically dependent isolation. Similarly, isolates of TYLCV-OM originating from Oman showed greater genetic variability than TYLCV-OM variants from Iran. Major recombination events, which were detected in all strains of TYLCV had breakpoints initiating in the C1, C1/C4, C2/C3 and V1 open reading frames (ORFs) and ending at the non-coding region and the C1, C1/C2 and C3 ORFs. Hence, these regions have consistently served as hot spots for recombination worldwide during the evolution of all currently recognized isolates and strains of TYLCV. PMID:24068582

  7. Molecular Analysis of H7 Avian Influenza Viruses from Australia and New Zealand: Genetic Diversity and Relationships from 1976 to 2007▿ †

    PubMed Central

    Bulach, Dieter; Halpin, Rebecca; Spiro, David; Pomeroy, Laura; Janies, Daniel; Boyle, David B.

    2010-01-01

    Full-genome sequencing of 11 Australian and 1 New Zealand avian influenza A virus isolate (all subtype H7) has enabled comparison of the sequences of each of the genome segments to those of other subtype H7 avian influenza A viruses. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. On the basis of the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of the neuraminidase sequences from the H7N1, H7N3, and H7N7 genomes revealed the same region-based relationships. This pattern of independent evolution of Australian isolates is supported by the results of analysis of each of the six remaining genomic segments. These results, in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates, suggest that the maintenance host(s) is nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences, despite the occurrence of multiple neuraminidase types, suggests the existence of a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above. PMID:20668069

  8. 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. ...

  9. 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...

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

    PubMed

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

    2015-01-01

    Members of the genus Pleurotus, also commonly known as oyster mushroom, are well known for their socioeconomic and biotechnological potentials. Despite being one of the most important edible fungi, the scarce information about the genetic diversity of the species in natural populations has limited their sustainable utilization. A total of 71 isolates of Pleurotus species were collected from three natural populations: 25 isolates were obtained from Kakamega forest, 34 isolates from Arabuko Sokoke forest and 12 isolates from Mount Kenya forest. Amplified fragment length polymorphism (AFLP) was applied to thirteen isolates of locally grown Pleurotus species obtained from laboratory samples using five primer pair combinations. AFLP markers and internal transcribed spacer (ITS) sequences of the ribosomal DNA were used to estimate the genetic diversity and evaluate phylogenetic relationships, respectively, among and within populations. The five primer pair combinations generated 293 polymorphic loci across the 84 isolates. The mean genetic diversity among the populations was 0.25 with the population from Arabuko Sokoke having higher (0.27) diversity estimates compared to Mount Kenya population (0.24). Diversity between the isolates from the natural population (0.25) and commercial cultivars (0.24) did not differ significantly. However, diversity was greater within (89%; P > 0.001) populations than among populations. Homology search analysis against the GenBank database using 16 rDNA ITS sequences randomly selected from the two clades of AFLP dendrogram revealed three mushroom species: P. djamor, P. floridanus and P. sapidus; the three mushrooms form part of the diversity of Pleurotus species in Kenya. The broad diversity within the Kenyan Pleurotus species suggests the possibility of obtaining native strains suitable for commercial cultivation. PMID:25344263

  11. 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...

  12. Genetic diversity for aluminum tolerance in sorghum.

    PubMed

    Caniato, F F; Guimarães, C T; Schaffert, R E; Alves, V M C; Kochian, L V; Borém, A; Klein, P E; Magalhaes, J V

    2007-03-01

    Genetic variation for aluminum (Al) tolerance in plants has allowed the development of cultivars that are high yielding on acidic, Al toxic soils. However, knowledge of intraspecific variation for Al tolerance control is needed in order to assess the potential for further Al tolerance improvement. Here we focused on the major sorghum Al tolerance gene, Alt ( SB ), from the highly Al tolerant standard SC283 to investigate the range of genetic diversity for Al tolerance control in sorghum accessions from diverse origins. Two tightly linked STS markers flanking Alt ( SB ) were used to study the role of this locus in the segregation for Al tolerance in mapping populations derived from different sources of Al tolerance crossed with a common Al sensitive tester, BR012, as well as to isolate the allelic effects of Alt ( SB ) in near-isogenic lines. The results indicated the existence not only of multiple alleles at the Alt ( SB ) locus, which conditioned a wide range of tolerance levels, but also of novel sorghum Al tolerance genes. Transgressive segregation was observed in a highly Al tolerant breeding line, indicating that potential exists to exploit the additive or codominant effects of distinct Al tolerance loci. A global, SSR-based, genetic diversity analysis using a broader sorghum set revealed the presence of both multiple Alt ( SB ) alleles and different Al tolerance genes within highly related accessions. This suggests that efforts toward broadening the genetic basis for Al tolerance in sorghum may benefit from a detailed analysis of Al tolerance gene diversity within subgroups across a target population. PMID:17252254

  13. 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...

  14. [Genetic diversity and bone marrow transplantation].

    PubMed

    Marry, E

    2012-05-01

    The genetic origin of the patients, for whom a bone marrow transplantation has been proposed, is a key determinant in the possibility of identifying or not a compatible unrelated donor, and consequently in the possibility of performing the bone marrow transplantation. The required strict HLA compatibility, in the context of a bone marrow transplantation, increases the difficulty. A patient has one chance over four to have a compatible donor within his brothers and sisters, if any. This chance becomes one over a million, as an average, in the context of unrelated donor search. Taking into consideration the genetic history of the populations, their evolution and the large actual HLA diversity, the probability of finding an unrelated donor for a defined patient varies according to the frequency and the combination of the patient's HLA antigens, genetic markers inherited not only from his parents, but also from his ancestries. In the unrelated context, the HLA compatible donor most probably shares the same genetic history than the patient, and consequently belongs to the same population group. The study of the genetic of populations explains the difficulties in finding an unrelated compatible donor in the migrant populations, particularly those originated from Africa and from the middle east, due to their HLA specificities and to the small number of donors sharing the same origins registered on a volunteer bone marrow donors' file worldwide. PMID:22454281

  15. Genetic Diversity of Koala Retroviral Envelopes

    PubMed Central

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

    2015-01-01

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

  16. Genetic diversity of koala retroviral envelopes.

    PubMed

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

    2015-03-01

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

  17. [Genetic diversity of Sabina vulgaris populations at different succession stages].

    PubMed

    Hong, Yu; Wang, Lin-He; Zhang, Guosheng; Enhe, Bayaer; Liang, Xiaorong

    2006-11-01

    By means of random amplified polymorphic DNA markers, a molecular ecological study was made with Sabina vulgaris populations at 4 succession stages in Maowusu sandy grassland, aimed to reveal the relationships between molecular variation and succession stages. A total of 17 random primers were selected for amplification, and 190 repetitive loci were produced, of which, 173 were polymorphic. The data were analyzed by POPGENE 3. 2 Version 1. 31. The results showed that the genetic diversity of S. vulgaris populations was high, and changed with succession stages. The percentage of polymorphic loci in each S. vulgaris population ranged from 64.21% to 74.63%, with the highest in early succession stage Artemisia ordosica + S. vulgaris on semi-fixed sand dunes, and the lowest in sub-climax stage S. vulgaris on fixed dunes. The genetic differentiation among the populations was small (G(st) = 0.1761), and 82.39% of it was within the populations. Cluster analysis demonstrated that the populations at similar succession stage clustered together, suggesting that the genetic differentiation was closely related to succession stage. The genetic diversity indicated by Nei index ranged in 0. 2163 -0. 2564, and the gene flow (N(m) *) was 2.7972, indicating that more gene exchange occurred within the populations, which prevented the genetic differentiation among the populations at different succession stages. PMID:17269316

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

    PubMed

    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

  19. Genetic diversity and population structure of three Indian horse breeds.

    PubMed

    Chauhan, Mamta; Gupta, Ashok Kumar; Dhillon, Santosh

    2011-06-01

    The genetic relationships of three Indian horse breeds-Marwari, Spiti, and Kathiawari were studied by genotyping 96 individuals with 20 polymorphic microsatellite markers. A total of 157 alleles were detected across 20 polymorphic loci. The Marwari population showed the highest allelic diversity (A = 5.7 and Ar = 5.14), followed by Spiti (A = 4.9 and Ar = 4.74) and Kathiawari (A = 4.1 and Ar = 3.82). The gene diversity was highest in the Spiti population (He = 0.67), followed by Marwari (He = 0.66) and Kathiawari (He = 0.59). Within population inbreeding estimates (f) in Marwari, Spiti and Kathiawari breeds were 0.18, 0.08, and 0.07, respectively, suggesting high level of inbreeding in these breeds. Analysis of bottleneck revealed evidence of recent bottleneck in Spiti and Kathiawari populations. Pair-wise Fst analysis, AMOVA and assignment tests demonstrated high genetic differentiation and low gene flow between populations. The information about genetic diversity and population structure will be useful for the future development of effective breeding management in order to preserve these Indian horse breeds. PMID:21104137

  20. 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.

  1. High levels of genetic diversity in Penaeus monodon populations from the east coast of India.

    PubMed

    Khedkar, Gulab Dattarao; Reddy, A Chandrashekar; Ron, Tetszuan Benny; Haymer, David

    2013-01-01

    Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of genetic diversity in shrimp populations from a region of India that represents the main sources of new material for brood stocks. In our study of these populations the overall mean genetic diversity was 0.191. The highest level of genetic diversity (0.357) was observed in the Kakinada population, whereas the lowest diversity (0.0171) was observed in the Nellore population. The results also indicate that overall, the populations along the Andhra Pradesh coast are genetically diverse despite the fact that there is considerable gene flow between them. From the results, it is evident that east cost of India shows high genetic diversity among P. monodon broods and no evidence of loss of diversity due to excessive inbreeding. The fact that the genetic variability of these populations has been maintained, despite ten years of dependence on these broods, shows that at the present time there is no indication of over exploitation. PMID:24363984

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

    PubMed Central

    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 data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources. PMID:26355595

  3. 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 data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources. PMID:26355595

  4. 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. PMID:21833642

  5. 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 depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

  6. 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

  7. 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 diversity and genetic diversity interact to influence community structure may be critically important for predicting the consequences of biodiversity loss. PMID:23858643

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

    PubMed Central

    Porto, I.; Zubillaga, A. L.

    2012-01-01

    Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (0.75 SE). In addition, population genetic datasets from four species (Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 1035 randomly selected local donor colonies will retain at least 5090% of the genetic diversity of the original population. PMID:22833700

  9. 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. PMID:1940281

  10. 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

  11. 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

  12. Pandemic Spread of Cholera: Genetic Diversity and Relationships within the Seventh Pandemic Clone of Vibrio cholerae Determined by Amplified Fragment Length Polymorphism

    PubMed Central

    Lan, Ruiting; Reeves, Peter R.

    2002-01-01

    The seventh cholera pandemic started in 1961 and continues today. A collection of 45 seventh pandemic isolates of V. cholerae sampled over a 33-year period were analyzed by amplified fragment length polymorphism (AFLP) fingerprinting. All but four pairs and one set of three isolates were distinguished. AFLP revealed far more variation than ribotyping, which was until now the most useful method of revealing variation within the pandemic clone. Unfortunately, the ribotype variation observed is mainly due to recombination between the multiple copies of the rrn genes (R. Lan and P. R. Reeves, Microbiology 144:12131221, 1998), which makes changes susceptible to repeat occurrences and reversion. This AFLP study shows that particularly for the common ribotypes G and H, such events have indeed occurred. AFLP grouped most of the 45 isolates into two clusters. Cluster I consists mainly of strains from the 1960s and 1970s, while cluster II contains mainly strains from the 1980s and 1990s, revealing a temporal pattern of change in the clone. This is best seen in the relationships of the strains from Africa, which correlate with the epidemiology of epidemics on that continent. The data confirm independent introductions to Africa during the 1970s outbreak and reveal several other African introductions. In the 1991 cholera upsurge, isolates from the Southern and Eastern African epidemic focus are markedly different from those from the West African epidemic focus. An isolate from 1987 in Algeria was identical to the West epidemic isolates, suggesting that the strain was present in Africa at least 3 years before causing large outbreaks. These observations have major implications for our understanding of cholera epidemiology. PMID:11773113

  13. 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. PMID:24351057

  14. 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.

  15. 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, ...

  16. 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...

  17. [Genetic diversity of introduced natural enemy Agasicles hygrophila (Coleoptera: Chrysomelidae)].

    PubMed

    Han, Zheng; Zhao, Long-Long; Ma, Rui-Yan; Hao, Jiong; Jia, Dong

    2011-11-01

    Flea beetle Agasicles hygrophila Selman & Vogt, the most effective natural enemy of alligator weed Alternanthera philoxeroideis, is originated from South America, and has been introduced into China for more than 20 years to control the weed. In this study, the technique of random amplification of polymorphic DNA (RAPD) was applied to assess the genetic diversity of four A. hygrophila geographic populations in Guangzhou, Chongqing, Kunming, and Fuzhou of China, and, taking the population in Florida of US as the reference, the relationships between the genetic differentiation and geographic differentiation among and within the populations were explored at molecular level. Thirteen primers that produced clear and reproducible products were selected from 111 random primers to amplify the 25 samples of the five A. hygrophila populations. The total polymorphic rate was 42.0%, and the polymorphic rate of Florida population was significantly higher than that of four China populations. The genetic differentiation among the four China populations was 25.5%. The cluster analysis by UPGMA indicated that there was a positive correlation between the genetic distance and geographic distance of different A. hygrophila geographic populations. PMID:22303686

  18. The Effect and Relative Importance of Neutral Genetic Diversity for Predicting Parasitism Varies across Parasite Taxa

    PubMed Central

    Ruiz-Lpez, Mara Jos; Monello, Ryan J.; Gompper, Matthew E.; Eggert, Lori S.

    2012-01-01

    Understanding factors that determine heterogeneity in levels of parasitism across individuals is a major challenge in disease ecology. It is known that genetic makeup plays an important role in infection likelihood, but the mechanism remains unclear as does its relative importance when compared to other factors. We analyzed relationships between genetic diversity and macroparasites in outbred, free-ranging populations of raccoons (Procyon lotor). We measured heterozygosity at 14 microsatellite loci and modeled the effects of both multi-locus and single-locus heterozygosity on parasitism using an information theoretic approach and including non-genetic factors that are known to influence the likelihood of parasitism. The association of genetic diversity and parasitism, as well as the relative importance of genetic diversity, differed by parasitic group. Endoparasite species richness was better predicted by a model that included genetic diversity, with the more heterozygous hosts harboring fewer endoparasite species. Genetic diversity was also important in predicting abundance of replete ticks (Dermacentor variabilis). This association fit a curvilinear trend, with hosts that had either high or low levels of heterozygosity harboring fewer parasites than those with intermediate levels. In contrast, genetic diversity was not important in predicting abundance of non-replete ticks and lice (Trichodectes octomaculatus). No strong single-locus effects were observed for either endoparasites or replete ticks. Our results suggest that in outbred populations multi-locus diversity might be important for coping with parasitism. The differences in the relationships between heterozygosity and parasitism for the different parasites suggest that the role of genetic diversity varies with parasite-mediated selective pressures. PMID:23049796

  19. 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

  20. 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.

  1. 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. PMID:26690525

  2. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla.

    PubMed

    Sood, A; Prasanna, R; Prasanna, B M; Singh, P K

    2008-01-01

    The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc. PMID:18481216

  3. 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. PMID:26895027

  4. 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. PMID:23985385

  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. 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. PMID:25327780

  7. Genetic and environmental influences on marital relationships.

    PubMed

    Spotts, Erica L; Neiderhiser, Jenae M; Towers, Hilary; Hansson, Kjell; Lichtenstein, Paul; Cederblad, Marianne; Pederson, Nancy L; Reiss, David

    2004-03-01

    As most adults will marry at least once during their lifetime, studying marital quality and its predictors is of great importance. The current study addresses (a) the extent of agreement between husbands and wives on their marital quality, (b) genetic and environmental sources of individual differences on spouse reports of marital quality, and (c) the extent to which genetic and environmental influences account for overlap of spouse reports on marital quality. Adult Swedish twin women and their partners participated in this study. Genotype-environment (GE) correlations were found for marital quality, suggesting that wives' genetically influenced characteristics set a tone for the marriage. Wives' genetically influenced characteristics also accounted for overlap of spouse reports of marital quality. Finally, nonshared environmental influences were the primary contributor to both individual reports and the overlap of spouse reports, an interesting deviation from findings of behavior genetic studies of other types of relationships. PMID:14992614

  8. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity.

    PubMed

    Renzette, Nicholas; Kowalik, Timothy F; Jensen, Jeffrey D

    2016-01-01

    A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms. PMID:26211679

  9. Multiple paternity does not depend on male genetic diversity

    PubMed Central

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

    2014-01-01

    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. PMID:25018559

  10. 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. PMID:25018559

  11. Genetic Diversity and Population Differentiation of Calanthe tsoongiana, a Rare and Endemic Orchid in China

    PubMed Central

    Qian, Xin; Wang, Cai-xia; Tian, Min

    2013-01-01

    Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species. PMID:24129175

  12. Environmental factors influence both abundance and genetic diversity in a widespread bird species.

    PubMed

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-11-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  13. Environmental factors influence both abundance and genetic diversity in a widespread bird species

    PubMed Central

    Liu, Yang; Webber, Simone; Bowgen, Katharine; Schmaltz, Lucie; Bradley, Katharine; Halvarsson, Peter; Abdelgadir, Mohanad; Griesser, Michael

    2013-01-01

    Genetic diversity is one of the key evolutionary variables that correlate with population size, being of critical importance for population viability and the persistence of species. Genetic diversity can also have important ecological consequences within populations, and in turn, ecological factors may drive patterns of genetic diversity. However, the relationship between the genetic diversity of a population and how this interacts with ecological processes has so far only been investigated in a few studies. Here, we investigate the link between ecological factors, local population size, and allelic diversity, using a field study of a common bird species, the house sparrow (Passer domesticus). We studied sparrows outside the breeding season in a confined small valley dominated by dispersed farms and small-scale agriculture in southern France. Population surveys at 36 locations revealed that sparrows were more abundant in locations with high food availability. We then captured and genotyped 891 house sparrows at 10 microsatellite loci from a subset of these locations (N = 12). Population genetic analyses revealed weak genetic structure, where each locality represented a distinct substructure within the study area. We found that food availability was the main factor among others tested to influence the genetic structure between locations. These results suggest that ecological factors can have strong impacts on both population size per se and intrapopulation genetic variation even at a small scale. On a more general level, our data indicate that a patchy environment and low dispersal rate can result in fine-scale patterns of genetic diversity. Given the importance of genetic diversity for population viability, combining ecological and genetic data can help to identify factors limiting population size and determine the conservation potential of populations. PMID:24363897

  14. Genetic Diversity of Microsatellite Loci in Hierarchically Structured Populations

    PubMed Central

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

    2011-01-01

    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 FST, including Slatkin's RST. Our analytical approximations for FST and RST show that familiar relationships between Nem and FST or RST hold when migration and mutation rates are small. Using the exact expressions for FST and RST, our numerical results show that when migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to FST depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, RST is relatively insensitive to mutation rates and mutational models. The differing behaviors of RST and FST 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. PMID:21575649

  15. The Genetic Relationship between Indentical Twins.

    ERIC Educational Resources Information Center

    Herman, Rosemary

    1984-01-01

    Reviews current research on a woman's chances of bearing twins and the genetic relationship, prenatal competition, and personality similarities between twins. In addition, the nature/nurture controversy is discussed in terms of evidence from studies of identical twins reared apart. Future studies are suggested to discover the ways twinning might

  16. Genetic diversity of canine olfactory receptors

    PubMed Central

    Robin, Stphanie; Tacher, Sandrine; Rimbault, Maud; Vaysse, Amaury; Drano, Stphane; Andr, Catherine; Hitte, Christophe; Galibert, Francis

    2009-01-01

    Background Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47%) of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life. PMID:19144169

  17. Interethnic Relationships: The Role of Social Network Diversity

    ERIC Educational Resources Information Center

    Clark-Ibanez, Marisol; Felmlee, Diane

    2004-01-01

    We examine the degree to which ethnic diversity in social networks relates to the frequency of interethnic romantic relationships for 318 college students. In a multi-nomial logit, we find that the odds of having an interethnic relationship once or twice, versus never, increase significantly if the respondent has a relatively ethnically diverse

  18. Plant species diversity and composition of experimental grasslands affect genetic differentiation of Lolium perenne populations.

    PubMed

    Nestmann, S; Sretenovic Rajicic, T; Dehmer, K J; Fischer, M; Schumacher, J; Roscher, C

    2011-05-01

    Contrasting hypotheses exist about the relationship between plant species diversity and genetic diversity. However, experimental data of species diversity effects on genetic differentiation among populations are lacking. To address this, Lolium perenne was sown with an equal number of seeds in 78 experimental grasslands (Jena Experiment) varying in species richness (1, 2, 4, 8 to 16) and functional group richness and composition (1-4; grasses, legumes, small herbs, tall herbs). Population sizes were determined 4years after sowing, and single-nucleotide polymorphism (SNP) DNA markers based on bulk samples of up to 100 individuals per population were applied. Genetic distances between the field populations and the initially sown seed population increased with sown species richness. The degree of genetic differentiation from the original seed population was largely explained by actual population sizes, which suggests that genetic drift was the main driver of differentiation. Weak relationships among relative allele frequencies and species diversity or actual population sizes, and a positive correlation between actual population sizes and expected heterozygosity also supported the role of genetic drift. Functional composition had additional effects on genetic differentiation of L. perenne populations, indicating a selection because of genotype-specific interactions with other species. Our study supports that genetic diversity is likely to be lower in plant communities with a higher number of interspecific competitors. Negative effects of species richness on population sizes may increase the probability of genetic drift, and selection because of genotype-specific interactions depending on species and genotypic community composition may modulate this relationship. PMID:21352387

  19. Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.

    PubMed

    Stensvold, Christen Rune; Clark, C Graham; Röser, Dennis

    2013-08-01

    Dientamoeba fragilis is a common intestinal parasite of unsettled clinical significance. Differences in clinical outcome of parasitic infections may reflect parasite genetic diversity, and so tools to study intra-genetic diversity that could potentially reflect differences in clinical phenotypes are warranted. Here, we show that genetic analysis of three D. fragilis housekeeping genes enables clear distinction between the two known genotypes, but that integration of housekeeping genes in multi-locus sequencing tools for D. fragilis may have limited epidemiological and clinical value due to no further added genetic resolution. PMID:23681023

  20. 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. PMID:17251114

  1. 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

  2. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    PubMed

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea. PMID:26909914

  3. Genetic Diversity in Introduced Populations with an Allee Effect

    PubMed Central

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

    2014-01-01

    A phenomenon that strongly influences the demography of small introduced populations and thereby potentially their genetic diversity is the demographic Allee effect, a reduction in population growth rates at small population sizes. We take a stochastic modeling approach to investigate levels of genetic diversity in populations that successfully overcame either a strong Allee effect, in which populations smaller than a certain critical size are expected to decline, or a weak Allee effect, in which the population growth rate is reduced at small sizes but not negative. Our results indicate that compared to successful populations without an Allee effect, successful populations with a strong Allee effect tend to (1) derive from larger founder population sizes and thus have a higher initial amount of genetic variation, (2) spend fewer generations at small population sizes where genetic drift is particularly strong, and (3) spend more time around the critical population size and thus experience more genetic drift there. In the case of multiple introduction events, there is an additional increase in diversity because Allee-effect populations tend to derive from a larger number of introduction events than other populations. Altogether, a strong Allee effect can either increase or decrease genetic diversity, depending on the average founder population size. By contrast, a weak Allee effect tends to decrease genetic diversity across the entire range of founder population sizes. Finally, we show that it is possible in principle to infer critical population sizes from genetic data, although this would require information from many independently introduced populations. PMID:25009147

  4. [Genetic structure and genetic diversity of Artemisia annua varieties (strains) populations based on SCoT markers].

    PubMed

    Chen, Da-xia; Cui, Guang-lin; Zhang, Xue; Li, Long-yun

    2014-09-01

    To reveal the genetic diversity and genetic structure in Artemisia annua varieties (strains) populations, we detected the genetic polymorphism within and among eight varieties (strains) populations (192 individuals) by the approach of Start Codon Targeted Polymorphism (SCoT). The associated genetic parameters were calculated by POPGENE1.31 and the relationship was constructed based on UPGMA method. The results showed that, using 20 screened primers, a total of 145 bands were produced, of which 122 were polymorphic loci. At species level, there was a high level of genetic diversity among eight varieties (strains) populations (PPB = 84.1% ,H = 0.217 3 and H(sp) = 0.341 9). However, at the variety (strains) population level, genetic diversity was lower, the average of genetic parameters was PPB = 41.9%, H = 0.121 5, H(pop) = 0.186 8. The Nei's genetic differentiation coefficient was 0.441 0, indicate that most of the genetic variation in this species existed within the variety populations. The gene flow (N(m) = 0.633 9) was less among populations, indicating that the degree of genetic differentiation was higher. Genetic similarity coefficient were changed from 0.755 1 to 0.985 7. By clustering analysis, eight varieties (strains) were clustered into two major categories and it was also showed the same or similar genetic background varieties (strains) have a tendency to gather in the same group. Results suggest that, in variety breeding, breeders should strengthen the exchange of bred germplasm and increase mutual penetration of excellent genes, which would broaden the genetic base of A. annua. PMID:25522606

  5. Genetic diversity of potato determined by random amplified polymorphic DNA analysis.

    PubMed

    Demeke, T; Lynch, D R; Kawchuk, L M; Kozub, G C; Armstrong, J D

    1996-05-01

    The RAPD procedure was used to establish genetic diversity of 28 potato genotypes including siblings and genotypes with no immediate relationship. In addition amplified DNA from three parents and Solanum chacoense were compared with that from six progeny to determine the genetic relationships. Amplification of genomic DNA from the 28 genotypes using PCR and 12 decamer primers yielded 158 amplified DNA fragments, ranging in size from 490 to 3200 bp. A total of 128 unique RAPD fragments were observed among the 28 potato genotypes. Similarity measures and principal coordinate analysis generally reflected the expected trends in relationships of the full and half-sib potato genotypes. However there were important exceptions to this general trend and it appears that related varieties can be as genetically different as varieties with no immediate relationship. The data suggest that RAPD analysis used in conjunction with pedigree information can provide a superior measure of genetic divergence than analysis based solely on pedigree information. PMID:24178606

  6. Autism spectrum disorder genetics: diverse genes with diverse clinical outcomes.

    PubMed

    Talkowski, Michael E; Minikel, Eric Vallabh; Gusella, James F

    2014-01-01

    The last several years have seen unprecedented advances in deciphering the genetic etiology of autism spectrum disorders (ASDs). Heritability studies have repeatedly affirmed a contribution of genetic factors to the overall disease risk. Technical breakthroughs have enabled the search for these genetic factors via genome-wide surveys of a spectrum of potential sequence variations, from common single-nucleotide polymorphisms to essentially private chromosomal abnormalities. Studies of copy-number variation have identified significant roles for both recurrent and nonrecurrent large dosage imbalances, although they have rarely revealed the individual genes responsible. More recently, discoveries of rare point mutations and characterization of balanced chromosomal abnormalities have pinpointed individual ASD genes of relatively strong effect, including both loci with strong a priori biological relevance and those that would have otherwise been unsuspected as high-priority biological targets. Evidence has also emerged for association with many common variants, each adding a small individual contribution to ASD risk. These findings collectively provide compelling empirical data that the genetic basis of ASD is highly heterogeneous, with hundreds of genes capable of conferring varying degrees of risk, depending on their nature and the predisposing genetic alteration. Moreover, many genes that have been implicated in ASD also appear to be risk factors for related neurodevelopmental disorders, as well as for a spectrum of psychiatric phenotypes. While some ASD genes have evident functional significance, like synaptic proteins such as the SHANKs, neuroligins, and neurexins, as well as fragile x mental retardation-associated proteins, ASD genes have also been discovered that do not present a clear mechanism of specific neurodevelopmental dysfunction, such as regulators of chromatin modification and global gene expression. In its sum, the progress from genetic studies to date has been remarkable and increasingly rapid, but the interactive impact of strong-effect genetic lesions coupled with weak-effect common polymorphisms has not yet led to a unified understanding of ASD pathogenesis or explained its highly variable clinical expression. With an increasingly firm genetic foundation, the coming years will hopefully see equally rapid advances in elucidating the functional consequences of ASD genes and their interactions with environmental/experiential factors, supporting the development of rational interventions. PMID:24614762

  7. 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. PMID:26164681

  8. 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. PMID:24336928

  9. Assessing and broadening genetic diversity of a rapeseed germplasm collection.

    PubMed

    Wu, Jinfeng; Li, Feng; Xu, Kun; Gao, Guizhen; Chen, Biyun; Yan, Guixin; Wang, Nian; Qiao, Jiangwei; Li, Jun; Li, Hao; Zhang, Tianyao; Song, Weiling; Wu, Xiaoming

    2014-12-01

    Assessing the level of genetic diversity within a germplasm collection contributes to evaluating the potential for its utilization as a gene pool to improve the performance of cultivars. In this study, 45 high-quality simple sequence repeat (SSR) markers were screened and used to estimate the genetic base of a world-wide collection of 248 rapeseed (Brassica napus) inbred lines. For the whole collection, the genetic diversity of A genome was higher than that of C genome. The genetic diversity of C genome for the semi-winter type was the lowest among the different germplasm types. Because B. oleracea is usually used to broaden the genetic diversity of C genome in rapeseed, we evaluated the potential of 25 wild B. oleracea lines. More allelic variations and a higher genetic diversity were observed in B. oleracea than in rapeseed. One B. oleracea line and one oilseed B. rapa line were used to generate a resynthesized Brassica napus line, which was then crossed with six semi-winter rapeseed cultivars to produce 7 F1 hybrids. Not only the allele introgression but also mutations were observed in the hybrids, resulting in significant improvement of the genetic base. PMID:25914586

  10. Genetic Diversity in Cotton Out-Crossing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously we have reported on the finding of genetic differences in the abiotic stress tolerance of cotton pollen. Genetic differences in sensitivity to humidity were observed impacting pollen survival in dry environments. The present study evaluated out-crossing rates in cotton lines whose polle...

  11. Cotton gene flow: Genetic diversity in outcrossing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously we have reported on the finding of genetic differences in the abiotic stress tolerance of cotton pollen. Genetic differences in sensitivity to humidity were observed impacting pollen survival in dry environments. The present study evaluated out-crossing rates in cotton lines whose pollen ...

  12. Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

  13. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  14. Ginning Efficiency between Diverse Genetic Groups of Upland Cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rising cost of energy in ginning cotton necessitates the evaluation of a diverse array of germplasm, currently available, for improving ginning efficiency. The objective was to study genetic variability for net ginning energy requirement and speed of ginning among five diverse groups of upland c...

  15. Examining the Relationships among Coaching Staff Diversity, Perceptions of Diversity, Value Congruence, and Life Satisfaction

    ERIC Educational Resources Information Center

    Cunningham, George B.

    2009-01-01

    The purpose of this study was to examine relationships among coaching staff diversity, perceptions of diversity, value congruence, and life satisfaction. Data were collected from 71 coaching staffs (N = 196 coaches). Observed path analysis was used to examine the study predictions. Results indicate that actual staff diversity was positively…

  16. 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...

  17. The Kuroshio current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides.

    PubMed

    Nakajima, Yuichi; Matsuki, Yu; Lian, Chunlan; Fortes, Miguel D; Uy, Wilfredo H; Campos, Wilfredo L; Nakaoka, Masahiro; Nadaoka, Kazuo

    2014-12-01

    Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north-east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north-east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns. PMID:25384848

  18. The Role of Propagule Pressure, Genetic Diversity and Microsite Availability for Senecio vernalis Invasion

    PubMed Central

    Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge

    2013-01-01

    Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of invasive plants, a clear differentiation between initial emergence and subsequent survival to juvenile and adult stages is required. PMID:23437301

  19. Stress-related hormones and genetic diversity in sea otters (Enhydra lutris)

    USGS Publications Warehouse

    Larson, S.; Monson, D.; Ballachey, B.; Jameson, R.; Wasser, S.K.

    2009-01-01

    Sea otters (Enhydra lutris) once ranged throughout the coastal regions of the north Pacific, but were extirpated throughout their range during the fur trade of the 18th and 19th centuries, leaving only small, widely scattered, remnant populations. All extant sea otter populations are believed to have experienced a population bottleneck and thus have lost genetic variation. Populations that undergo severe population reduction and associated inbreeding may suffer from a general reduction in fitness termed inbreeding depression. Inbreeding depression may result in decreased testosterone levels in males, and reduced ability to respond to stressful stimuli associated with an increase in the stress-related adrenal glucocorticoid hormones, cortisol and corticosterone. We investigated correlations of testosterone, cortisol, and corticosterone with genetic diversity in sea otters from five populations. We found a significant negative correlation between genetic diversity and both mean population-level (r2 = 0.27, P < 0.001) and individual-level (r2 = 0.54, P < 0.001) corticosterone values, as well as a negative correlation between genetic diversity and cortisol at the individual level (r2 = 0.17, P = 0.04). No relationship was found between genetic diversity and testosterone (P = 0.57). The strength of the correlations, especially with corticosterone, suggests potential negative consequences for overall population health, particularly for populations with the lowest genetic diversity. ?? 2009 by the Society for Marine Mammalogy.

  20. 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. PMID:23360002

  1. Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred.

    PubMed

    Stkov-Jakabov, Daniela; Trandzk, J; Hudecov-Kvasnkov, L'udmila; Hegedsov-Zetochov, Erika; Bugarsk, A; Buleca, J; Zldg, L; Jakab, F; Fl'ak, P

    2004-01-01

    Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign F(IS) estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed. PMID:15379441

  2. 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

  3. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly.

    PubMed

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-11-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

  4. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly

    PubMed Central

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-01-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

  5. 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

  6. 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

    2016-01-01

    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

  7. The structural diversity of artificial genetic polymers.

    PubMed

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

    2016-02-18

    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

  8. 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

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

    PubMed

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

    2013-05-01

    As two major popular theories to explain evolutionary facts, the neutral theory and Neo-Darwinism, despite their proven virtues in certain areas, still fail to offer comprehensive explanations to such fundamental evolutionary phenomena as the genetic equidistance result, abundant overlap sites, increase in complexity over time, incomplete understanding of genetic diversity, and inconsistencies with fossil and archaeological records. Maximum genetic diversity hypothesis (MGD), however, constructs a more complete evolutionary genetics theory that incorporates all of the proven virtues of existing theories and adds to them the novel concept of a maximum or optimum limit on genetic distance or diversity. It has yet to meet a contradiction and explained for the first time the half-century old Genetic Equidistance phenomenon as well as most other major evolutionary facts. It provides practical and quantitative ways of studying complexity. Molecular interpretation using MGD-based methods reveal novel insights on the origins of humans and other primates that are consistent with fossil evidence and common sense, and reestablished the important role of China in the evolution of humans. MGD theory has also uncovered an important genetic mechanism in the construction of complex traits and the pathogenesis of complex diseases. We here made a series of sequence comparisons among yeasts, fishes and primates to illustrate the concept of limit on genetic distance. The idea of limit or optimum is in line with the yin-yang paradigm in the traditional Chinese view of the universal creative law in nature. PMID:23732666

  10. Genetic diversity and interrelationship among mulberry genotypes.

    PubMed

    Banerjee, Rita; Roychowdhuri, Sukhen; Sau, Haradhan; Das, Bimal Kumar; Ghosh, Pannalal; Saratchandra, Beera

    2007-08-01

    Fourteen morphometric traits were used to examine the genetic divergence of 25 mulberry (Morus spp.) genotypes from varied agroclimatic conditions of India. Wide variation was observed for all the traits. The genotypes irrespective of their place of collection were grouped into 10 different clusters. Seven accessions, that is, Baragura-2, Gorabandha-2, Kalimpong, Herbertpur, Kollegal, Resham majri-7, and UP-14 each a cluster of unique entries will be of useful for genetic resources. Nevertheless, the correlation and path analysis suggest the direct selection of lamina length, fresh leaf weight, leaf area, and single leaf weight will be rewarding for mulberry leaf yield improvement. PMID:17707213

  11. Regional specificity of genetically diverse garlic varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Garlic is a profitable crop for small to medium-sized vegetable farmers. Despite the increasing market for specialty garlic, it is remarkable how little is known about the diverse types of garlic available. Farmers need to know which garlic types perform well under their growing conditions, and th...

  12. Genetic relationships within and between Capsicum species.

    PubMed

    Ince, Ay?e Gul; Karaca, Mehmet; Onus, A Naci

    2010-02-01

    Genetic relationships were estimated among 24 accessions belonging to 11 species of Capsicum, using 2,760 RAPD markers based on touch-down polymerase chain reactions (Td-RAPD-PCR). These markers were implemented in analyses of principal coordinates, unweighted pair group mean average, and 2,000 bootstrap replications. The accessions were divided into four groups, corresponding to previously described Capsicum complexes: C. annuum complex (CA), C. baccatum complex (CB), C. pubescens complex (CP), and C. chacoense accessions (CA/B). Their overall mean genetic similarity index was 0.487 +/- 0.082, ranging from 0.88 to 0.32, based on Jaccard's coefficient. The highest genetic variation was observed among the accessions in CP; the accessions in CB had a low level of variation as judged from the standard deviations of the genetic similarity indices. Based on the Td-RAPD-PCR markers, the 24 accessions were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Accessions of C. chacoense were found to be equally related to complexes CA, CB, and CP. PMID:19916044

  13. 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. PMID:24012599

  14. 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...

  15. Genetic Diversity for Aluminum Tolerance in Sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Significant genetic variation for aluminum (Al) tolerance in many plant species has allowed the development of cultivars that are high yielding on acidic, Al toxic soils. However, knowledge of intraspecific variation for Al tolerance control is needed in order to assess the potential for further Al ...

  16. The Host Genetic Diversity in Malaria Infection

    PubMed Central

    de Mendona, Vitor R. R.; Goncalves, Marilda Souza; Barral-Netto, Manoel

    2012-01-01

    Populations exposed to Plasmodium infection develop genetic mechanisms of protection against severe disease. The clinical manifestation of malaria results primarily from the lysis of infected erythrocytes and subsequent immune and inflammatory responses. Herein, we review the genetic alterations associated with erythrocytes or mediators of the immune system, which might influence malaria outcome. Moreover, polymorphisms in genes related to molecules involved in mechanisms of cytoadherence and their influence on malaria pathology are also discussed. The results of some studies have suggested that the combinatorial effects of a set of genetic factors in the erythrocyte-immunology pathway might be relevant to host resistance or susceptibility against Plasmodium infection. However, these results must be interpreted with caution because of the differences observed in the functionality and frequency of polymorphisms within different populations. With the recent advances in molecular biology techniques, more robust studies with reliable data have been reported, and the results of these studies have identified individual genetic factors for consideration in preventing severe disease and the individual response to treatment. PMID:23316245

  17. 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...

  18. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Utilization of crop diversity held in genebanks is dependent on knowledge of useful traits including those identified genotypically. Target region amplification polymorphism (TRAP) markers were used to evaluate the genetic diversity and relationship among a sample of 263 chickpea landrace germplasm ...

  19. Genetic Diversity among Ancient Nordic Populations

    PubMed Central

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

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (?2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type diluted by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,3003,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  20. Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system.

    PubMed

    Doa, Jorge; Moreno-Garca, Marina; Criscione, Charles D; Serrano, David; Jovani, Roger

    2015-12-01

    Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host-symbiont systems. Here, we studied mtDNA variation in a host-symbiont non-model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star-like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes. PMID:26811755

  1. Glacial refugia and modern genetic diversity of 22 western North American tree species.

    PubMed

    Roberts, David R; Hamann, Andreas

    2015-04-01

    North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  2. 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.

    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.

  3. Evaluation of genetic and functional diversity of Stenotrophomonas isolates from diverse effluent treatment plants.

    PubMed

    Verma, Vinita; Raju, Sajan C; Kapley, Atya; Kalia, Vipin Chandra; Daginawala, Hatim F; Purohit, Hemant J

    2010-10-01

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

  4. Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management.

    PubMed

    Archie, Elizabeth A; Chiyo, Patrick I

    2012-02-01

    Genetic tools are increasingly valuable for understanding the behaviour, evolution, and conservation of social species. In African elephants, for instance, genetic data provide basic information on the population genetic causes and consequences of social behaviour, and how human activities alter elephants' social and genetic structures. As such, African elephants provide a useful case study to understand the relationships between social behaviour and population genetic structure in a conservation framework. Here, we review three areas where genetic methods have made important contributions to elephant behavioural ecology and conservation: (1) understanding kin-based relationships in females and the effects of poaching on the adaptive value of elephant relationships, (2) understanding patterns of paternity in elephants and how poaching can alter these patterns, and (3) conservation genetic tools to census elusive populations, track ivory, and understand the behavioural ecology of crop-raiding. By comparing studies from populations that have experienced a range of poaching intensities, we find that human activities have a large effect on elephant behaviour and genetic structure. Poaching disrupts kin-based association patterns, decreases the quality of elephant social relationships, and increases male reproductive skew, with important consequences for population health and the maintenance of genetic diversity. In addition, we find that genetic tools to census populations or gather forensic information are almost always more accurate than non-genetic alternatives. These results contribute to a growing understanding of poaching on animal behaviour, and how genetic tools can be used to understand and conserve social species. PMID:21880086

  5. Genetic diversity of Acanthamoeba isolates from ocean sediments

    PubMed Central

    Liu, Hua; Ha, Young-Ran; Lee, Sung-Tae; Hong, Yean-Chul; Kong, Hyun-Hee

    2006-01-01

    Genetic diversity of 18 Acanthamoeba isolates from ocean sediments was evaluated by comparing mitochondrial (mt) DNA RFLP, 18S rDNA sequences and by examining their cytopathic effects on human corneal epithelial cells versus reference strains. All isolates belonged to morphologic group II. Total of 16 restriction phenotypes of mtDNA from 18 isolates demonstrated the genetic diversity of Acanthamoeba in ocean sediments. Phylogenetic analysis using 18s rDNA sequences revealed that the 18 isolates were distinct from morphological groups I and III. Fifteen isolates showed close relatedness with 17 clinical isolates and A. castellanii Castellani and formed a lineage equivalent to T4 genotype of Byers' group. Two reference strains from ocean sediment, A. hatchetti BH-2 and A. griffini S-7 clustered unequivocally with these 15 isolates. Diversity among isolates was also evident from their cytopathic effects on human corneal cells. This is the first time describing Acanthamoeba diversity in ocean sediments in Korea. PMID:16809959

  6. Biased morph ratios and skewed mating success contribute to loss of genetic diversity in the distylous Pulmonaria officinalis

    PubMed Central

    Meeus, Sofie; Honnay, Olivier; Brys, Rein; Jacquemyn, Hans

    2012-01-01

    Background and Aims In heterostylous plant species, skewed morph ratios are not uncommon and may arise from a range of factors. Despite the recognized importance of skewed morph ratios on overall reproductive success within populations, little is known about the impact of skewed morph ratios on population genetic diversity and differentiation in heterostylous species. This study specifically aimed to clarify the effect of population size and morph bias on population genetic diversity and differentiation in the temperate forest herb Pulmonaria officinalis. This species is characterized by a distylous breeding system and shows morph-specific differences in reproductive success. Methods Genetic diversity was determined for 27 P. officinalis populations in northern Belgium by using eight recently developed microsatellite markers. Multiple regressions were used to assess the relationship between genetic diversity, morph bias and population size, and FST-values were calculated for short- and long-styled morphs separately to study genetic differentiation as a function of morph type. Key Results For all genetic measures used, morph bias was more important in explaining patterns of genetic diversity than population size, and in all cases patterns of population genetic diversity followed a quadratic function, which showed a symmetrical decrease in genetic diversity with increasing morph bias. However, probably due to the reproductive advantage of L-morphs relative to S-morphs, maximum genetic diversity was found in populations showing an excess of L-morphs (607 % L-morph). On the other hand, no significant difference in pairwise genetic distances between populations was observed between L- (0107) and S-morphs (0106). Conclusions Our results indicate that significant deviations from equal morph ratios not only affect plant reproductive success but also population genetic diversity of heterostylous plant species. Hence, when defining conservation measures for populations of heterostylous plant species, morph ratios should be considered as an important trait affecting their long-term population viability. PMID:22021814

  7. Genetic diversity among ancient Nordic populations.

    PubMed

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

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  8. 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

  9. 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

  10. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    NASA Astrophysics Data System (ADS)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  11. Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

    PubMed

    Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

    2010-08-01

    Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads. PMID:20151984

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

    PubMed

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

    2016-01-01

    Paragonimiasis caused by lung flukes (genus Paragonimus) is a neglected disease occurring in Asia, Africa and the Americas. The genus is species-rich, ancient and widespread. Genetic diversity is likely to be considerable, but investigation of this remains confined to a few populations of a few species. In recent years, studies of genetic diversity have moved from isoenzyme analysis to molecular phylogenetic analysis based on selected DNA sequences. The former offered better resolution of questions relating to allelic diversity and gene flow, whereas the latter is more suitable for questions relating to molecular taxonomy and phylogeny. A picture is emerging of a highly diverse taxon of parasites, with the greatest diversity found in eastern and southern Asia where ongoing speciation might be indicated by the presence of several species complexes. Diversity of lung flukes in Africa and the Americas is very poorly sampled. Functional molecules that might be of value for immunodiagnosis, or as targets for medical intervention, are of great interest. Characterisation of these from Paragonimus species has been ongoing for a number of years. However, the imminent release of genomic and transcriptomic data for several species of Paragonimus will dramatically increase the rate of discovery of such molecules, and illuminate their diversity within and between species. PMID:26740357

  13. Genetic diversity and conservation in a small endangered horse population.

    PubMed

    Janova, Eva; Futas, Jan; Klumplerova, Marie; Putnova, Lenka; Vrtkova, Irena; Vyskocil, Mirko; Frolkova, Petra; Horin, Petr

    2013-08-01

    The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population. PMID:23649723

  14. 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. PMID:26526745

  15. Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.

    PubMed

    Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

    2015-01-01

    Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. PMID:25468001

  16. Genetic diversity of Centella asiatica in China analyzed by inter-simple sequence repeat (ISSR) markers: combination analysis with chemical diversity.

    PubMed

    Zhang, Xiao-Gang; Han, Ting; He, Zhi-Gao; Zhang, Qiao-Yan; Zhang, Lei; Rahman, Khalid; Qin, Lu-Ping

    2012-01-01

    Centella asiatica is an important plant species used in traditional Chinese medicine. To help the efficient use and conservation of this species, the genetic diversity of C. asiatica populations in China was investigated using inter-simple sequence repeat (ISSR) markers. Fourteen natural populations comprising 162 individuals were included to estimate genetic diversity. At the species level, genetic diversity was relatively high (P = 66.33%, H = 0.2183, I = 0.3305). At the population level, the genetic diversity of JH (Jinhua, Zhejiang Province, China) and JJ (Jiujiang, Jiangxi Province, China) populations was relatively high (P = 43.88%, 38.78%, H = 0.1610, 0.1301, I = 0.2376, 0.1957, respectively), whereas the genetic diversity of GA (Guang'an, Sichuan Province, China) and EM (E'mei, Sichuan Province, China) was relatively low (P = 10.2%, 5.1%, H = 0.0383, 0.0211, I = 0.0570, 0.0309, respectively). On the basis of Nei's G(st) value, more genetic differentiation among populations was determined (G(st) = 0.6573). In addition, the 14 populations were clustered into four groups in view of abundant ISSR data, which further defined the genetic relationship among populations. Interestingly, the genetic clustering result was similar to previous chemical clustering results based on high-performance liquid chromatography (HPLC) data, which would also classify the 14 populations into four groups. Thus, we combined the clustering results and compared their difference. The combined analysis and genetic diversity data provide a scientific basis for conserving populations of relatively high genetic diversity such as JH and JJ populations and establishing good agricultural practices (GAP) for C. asiatica. PMID:21853385

  17. Genetic Diversity in the Paramecium aurelia Species Complex

    PubMed Central

    Catania, Francesco; Wurmser, Franois; Potekhin, Alexey A.; Przybo?, Ewa; Lynch, Michael

    2009-01-01

    Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterizedreproductively and geneticallyworldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex. PMID:19023087

  18. 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...

  19. Strength in Diversity: Hidden Genetic Depths of Mycobacterium tuberculosis.

    PubMed

    Sampson, Samantha L

    2016-02-01

    Next-generation whole genome sequencing data is currently being utilised to explore Mycobacterium tuberculosis genetic diversity. Studies have focused in particular on the evolution of drug resistance, and have revealed a surprising degree of dynamic population heterogeneity, with implications for transmission studies, treatment regimens and new drug target development. PMID:26755442

  20. 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...

  1. Genetic resources and genomic diversity in the perennial triticeae grasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The perennial Triticeae grasses comprise hundreds of diverse species, organized into genomically defined genera based on chromosome pairing studies of interspecific hybrids. Our objective is to develop expressed gene sequence tag (EST) markers and genetic maps for these divergent genomes to further...

  2. GENETIC DIVERSITY OF CANADA THISTLE (CIRSIUM ARVENSE) IN NORTH DAKOTA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Canada thistle, Cirsium arvense, is a noxious weed that occurs in a wide range of habitats and is difficult to control due to its extensive root system and prolific seed production. Here, we focused on estimating the level of genetic diversity between populations in North Dakota as a first step in e...

  3. 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

  4. 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...

  5. CURRENT EFFORTS IN CONSERVATION OF ANIMAL GENETIC DIVERSITY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Changing consumer demand, threat of disease, and contraction of genetic diversity drive the need to establish vibrant livestock conservation activities. For effective in-situ and ex-situ conservation strategies to function, dialogue and synergistic action between public and private sectors must occu...

  6. 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 ...

  7. Molecular genetic diversity of Satureja bachtiarica.

    PubMed

    Saidi, Mehdi; Movahedi, Khavar; Mehrabi, Ali Ashraf; Kahrizi, Danial

    2013-11-01

    Fifty-seven genotypes from eight population of Satureja bachtiarica was evaluated using fifteen ISSR and eleven RAPD markers. DNA profiling using RAPD primers amplified 84 loci, among which 81 were polymorphic with an average of 7.36 polymorphic fragments per locus. Also, using RAPD markers maximum and minimum polymorphic bands observed for Semyrom (77.38 %) and Farsan (40.48 %) populations, respectively. Semyrom population recorded the highest unbiased expected heterozygosity (0.259) and Shannon's Indices (0.38). While, the lowest values of unbiased expected heterozygosity (0.172) and Shannon's Index (0.245) were recorded for Eghlid and Farsan populations, respectively. On the other hand, ISSR primers produced 136 bands, from which 134 were polymorphic with an average of 9.06 polymorphic fragments per primer (98.52 %). The ISSR markers evaluation revealed that maximum and minimum polymorphic bands observed for Semyrom (66.18 %) and Farsan (31.62 %), respectively. Shahrekorud population recorded the highest unbiased expected heterozygosity (0.211) and Shannon's Indices (0.301). While, the lowest value of unbiased expected heterozygosity (0.175) observed for Farsan and Yazd populations and the lowest Shannon's Index (0.191) recorded by Farsan population. The overall results of the study revealed that both ISSR and RAPD markers were effective for evaluation of genetic variation of S. bachtiarica. PMID:24096911

  8. 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

    2016-01-01

    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

  9. 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

  10. Population genetic structure and genetic diversity of soybean aphids from USA, Korea and Japan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of USA. Very little is known about the population genetic structure and genetic diversity of the soybean ap...

  11. Inferring recent historic abundance from current genetic diversity.

    PubMed

    Palsbll, Per J; Zachariah Peery, M; Olsen, Morten T; Beissinger, Steven R; Brub, Martine

    2013-01-01

    Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only. PMID:23181682

  12. Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan.

    PubMed

    Naeem, Asif; Hosomi, Takushi; Nishimura, Yorihiro; Alam, Muhammad Masroor; Oka, Tomoichiro; Zaidi, Syed Sohail Zahoor; Shimizu, Hiroyuki

    2014-09-01

    Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5' untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler's murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41-56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV. PMID:24899154

  13. Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation

    PubMed Central

    gisdttir, Hafds Hanna; Kuss, Patrick; Stcklin, Jrg

    2009-01-01

    Background and Aims Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity. Methods Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure. Key Results High within-population genetic diversity (HE = 076) and a relatively low inbreeding coefficient (FIS = 0022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G?ST = 053). A significant isolation-by-distance relationship was found (r = 062, P < 0001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population. Conclusions The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear westerneastern differentiation in this species merits consideration in future conservation efforts. PMID:19797423

  14. Genetic (RAPD) diversity in Peromyscus maniculatus populations in a naturally fragmented landscape.

    PubMed

    Vucetich, L M; Vucetich, J A; Joshi, C P; Waite, T A; Peterson, R O

    2001-01-01

    We assessed the effects of long-term habitat fragmentation on genetic (random amplified polymorphic DNA) diversity in 11 Peromyscus maniculatus populations in the Lake Superior watershed. We analysed genetic structure at two spatial scales and the effect of island size and isolation on genetic diversity. At the regional scale, island populations differed from mainland populations (FST = 0.36), but mainland populations did not differ from each other (FST = 0.01). At the local scale, populations of the main island of Isle Royale differed from adjacent islet populations (P < 0.001; Monte Carlo approximation of Fisher's exact test), but not from each other (combined P = 0.63). Although geographical distance and genetic distance were positively correlated (P < 0.01; Mantel test), cluster analysis revealed some inconsistencies. Finally, genetic diversity was inversely related to isolation (P = 0.01), but had an unexpectedly negative relationship with island area (P = 0.03). The genetic structure of P. maniculatus populations in portions of the Lake Superior watershed appears to have been affected by long-term habitat fragmentation. PMID:11251785

  15. Molecular genetic relationships of the salmonellae.

    PubMed Central

    Boyd, E F; Wang, F S; Whittam, T S; Selander, R K

    1996-01-01

    A multilocus enzyme electrophoresis analysis of 96 strains of the salmonellae distinguished 80 electrophoretic types (ETs) and placed them in eight groups, seven of which correspond precisely to the seven taxonomic groups (I, II, IIIa, IIIb, IV, V, and VI) previously defined on the basis of biotype and genomic DNA hybridization. In addition, multilocus enzyme electrophoresis identified an eighth distinctive group (designated VII) composed of five strains that had been assigned to group IV on the basis of biotype. An analysis of variation in the combined nucleotide sequences of five housekeeping genes among 16 strains representing all eight groups yielded estimates of overall genetic relationships that are fully consistent with those indicated by DNA hybridization. However, the nucleotide sequences of seven invasion genes (inv/spa) in the strains of group VII were closely similar to those of strains of group IV. These findings are interpreted as evidence that group VII represents an old, differentiated lineage to which one or more large parts of the chromosomal genome of the group IV lineage, including the 40-kb segment on which the invasion genes are located, have been horizontally transferred. All lines of molecular genetic evidence indicate that group V is very strongly differentiated from all other groups, thus supporting its current taxonomic treatment as a species, Salmonella bongori, separate from S. enterica. The Salmonella Reference Collection C, composed of the 16 strains used in DNA sequence studies, has been established for research on variation in natural populations. PMID:8975610

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

    PubMed

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

    2013-01-01

    A major objective of synthetic biology is to make the process of designing genetically encoded biological systems more systematic, predictable, robust, scalable, and efficient. Examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from simple genetic switches to search-and-destroy systems. While significant advances in DNA synthesis capabilities support the construction of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Thus, while synthetic biology offers much promise in developing systems to address challenges faced in the fields of manufacturing, environment and sustainability, and health and medicine, 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

  17. 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

  18. [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. PMID:17035182

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

    PubMed

    Shao, Yafang; Bao, Jinsong

    2015-08-01

    Polyphenols, such as phenolic acid, anthocyanin and proanthocyanidins, have both nutraceutical properties and functional significance for human health. Identification of polyphenolic compounds and investigation of their genetic basis among diverse rice genotypes provides the basis for the improvement of the nutraceutical properties of whole rice grain. This review focuses on current information on the identification, genetic diversity, formation and distribution patterns of the phenolic acid, anthocyanin, and proanthocyanidins in whole rice grain. The genetic analysis of polyphenol content and antioxidant capacity allows the identification of several candidate genes or quantitative trait loci (QTL) responsible for polyphenol variation, which may be useful in improvement of these phytochemicals by breeding. Future challenges such as how to mitigate the effects of climate change while improving nutraceutical properties in whole grain, and how to use new technology to develop new rice high in nutraceutical properties are also presented. PMID:25766805

  20. 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

  1. Extraordinary Genetic Diversity in a Wood Decay Mushroom

    PubMed Central

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

    2015-01-01

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

  2. Extraordinary Genetic Diversity in a Wood Decay Mushroom.

    PubMed

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

    2015-10-01

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

  3. 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...

  4. High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation

    PubMed Central

    Buckland, Steeves; Cole, Nik C.; Groombridge, Jim J.; Küpper, Clemens; Burke, Terry; Dawson, Deborah A.; Gallagher, Laura E.; Harris, Stephen

    2014-01-01

    Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708

  5. Individual genetic diversity and probability of infection by avian malaria parasites in blue tits (Cyanistes caeruleus).

    PubMed

    Ferrer, E S; Garca-Navas, V; Sanz, J J; Ortego, J

    2014-11-01

    Understanding the importance of host genetic diversity for coping with parasites and infectious diseases is a long-standing goal in evolutionary biology. Here, we study the association between probability of infection by avian malaria (Plasmodium relictum) and individual genetic diversity in three blue tit (Cyanistes caeruleus) populations that strongly differ in prevalence of this parasite. For this purpose, we screened avian malaria infections and genotyped 789 blue tits across 26 microsatellite markers. We used two different arrays of markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found a significant relationship between probability of infection and host genetic diversity estimated at the subset of neutral markers that was not explained by strong local effects and did not differ among the studied populations. This relationship was not linear, and probability of infection increased up to values of homozygosity by locus (HL) around 0.15, reached a plateau at values of HL from 0.15 to 0.40 and finally declined among a small proportion of highly homozygous individuals (HL > 0.4). We did not find evidence for significant identity disequilibrium, which may have resulted from a low variance of inbreeding in the study populations and/or the small power of our set of markers to detect it. A combination of subtle positive and negative local effects and/or a saturation threshold in the association between probability of infection and host genetic diversity in combination with increased resistance to parasites in highly homozygous individuals may explain the observed negative quadratic relationship. Overall, our study highlights that parasites play an important role in shaping host genetic variation and suggests that the use of large sets of neutral markers may be more appropriate for the study of heterozygosity-fitness correlations. PMID:25264126

  6. Diversity and genetic structure analysis of three Amazonian Amerindian populations of Colombia.

    PubMed Central

    Braga, Yamid; Arias B, Leonardo

    2012-01-01

    Introduction: In the departments of the Vaupés and Guaviare, in southeastern Colombia, in a transitional area between Amazonia and the eastern plains, inhabit indigenous groups belonging to the Tukanoan (East) and Guahiban linguistic families. Although some studies have dealt with the culture and the cosmology description of these groups, little research has been done on the biological diversity and genetic relationships of such groups. Objective: To estimate the diversity, the structure, and the genetic relationships of one Guahiban and two Tukanoan groups of the Colombian Amazonian region. Methods: Samples were collected (n = 106) from unrelated individuals belonging to the Vaupés native indigenous communities. The DNA was extracted and nine autosomal microsatellites were typed. Several measures of diversity, FST, pairwise FST, and population differentiation between groups were calculated. Finally, it was estimated the genetic distances of the groups studied in relation with other Amazonian, Andean and Central American indigenous people. Results: 1. The genetic diversity found stands within the range of other Amazonian populations, whereas compared to the mestizo and afro-descendant Colombian populations, such diversity showed to be lower. 2. The structure and population differentiation tests showed two clusters; one consisting of the Vaupés Tukanoan and Guaviare Tukanoan groups, and a second one formed by the Guayabero. 3. Tukanoan groups are found to be closer related to the Brazilian Amazonian populations than to the Guayabero. Conclusion: The results of this study suggest that the Guayabero group from Guaviare, are genetically differentiated from those Tukanoan groups of the Vaupés and Guaviare. PMID:24893054

  7. Molecular identification and genetic relationships of Palestinian grapevine cultivars.

    PubMed

    Basheer-Salimia, Rezq; Lorenzi, Silvia; Batarseh, Fadi; Moreno-Sanz, Paula; Emanuelli, Francesco; Grando, M Stella

    2014-06-01

    Palestine has a wide range of agro-ecological concerns and hosts a large variety of plants. Grapes are part of the cultural heritage and provide an indispensable food ingredient. Local cultivars have been traditionally identified on the basis of morphological traits, geographical origin, or names of the vineyard owner; therefore, the occurrence of homonymy, synonymy, and misnaming significantly prevents their valorization. DNA profiling by 22 common SSR markers was used to characterize 43 putative cultivars grown mainly for local table grape consumption at the southern highland regions of West-Bank, to further evaluate genetic diversity and relationships of the population. Consistent matching of SSR markers with grapevines cultivated in neighboring countries or maintained in European germplasm collections was found for 8 of the 21 different non-redundant genotypes discovered, suggesting possible synonyms as well as the occurrence of breeding selections formerly developed in the USA. Genetic relationships inferred from SSR markers clearly assigned Palestinian cultivars to the Proles orientalis subpr. Antasiatica ancestral population, and they even remarked the connection between local resources and cultivars generated from international table grape breeding. This study supports the value of collection and conservation of vines endemic to a region of immense historical importance for viticulture. PMID:24469973

  8. 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. PMID:17604574

  9. Genetic Diversity of Coastal Bottlenose Dolphins Revealed by Structurally and Functionally Diverse Hemoglobins

    PubMed Central

    Remington, Nicole; Stevens, Robert D.; Wells, Randall S.; Hohn, Aleta; Dhungana, Suraj; Taboy, Celine H.; Crumbliss, Alvin L.; Henkens, Robert; Bonaventura, Celia

    2007-01-01

    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 enhance 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 ? and ? 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. PMID:17604574

  10. Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design

    PubMed Central

    Bell, J.J; Okamura, B

    2005-01-01

    Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection. PMID:16024366

  11. Increased Extinction Potential of Insular Fish Populations with Reduced Life History Variation and Low Genetic Diversity

    PubMed Central

    Hellmair, Michael; Kinziger, Andrew P.

    2014-01-01

    Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species. PMID:25409501

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

    PubMed

    Hellmair, Michael; Kinziger, Andrew P

    2014-01-01

    Theoretical work has shown that reduced phenotypic heterogeneity leads to population instability and can increase extinction potential, yet few examples exist of natural populations that illustrate how varying levels expressed diversity may influence population persistence, particularly during periods of stochastic environmental fluctuation. In this study, we assess levels of expressed variation and genetic diversity among demographically independent populations of tidewater goby (Eucyclogobius newberryi), show that reductions in both factors typically coincide, and describe how low levels of diversity contribute to the extinction risk of these isolated populations. We illustrate that, for this annual species, continuous reproduction is a safeguard against reproductive failure by any one population segment, as natural, stochastically driven salinity increases frequently result in high mortality among juvenile individuals. Several study populations deviated from the natural pattern of year-round reproduction typical for the species, rendering those with severely truncated reproductive periods vulnerable to extinction in the event of environmental fluctuation. In contrast, demographically diverse populations are more likely to persist through such periods through the continuous presence of adults with broader physiological tolerance to abrupt salinity changes. Notably, we found a significant correlation between genetic diversity and demographic variation in the study populations, which could be the result of population stressors that restrict both of these diversity measures simultaneously, or suggestive of a causative relationship between these population characteristics. These findings demonstrate the importance of biocomplexity at the population level, and assert that the maintenance of diversity contributes to population resilience and conservation of this endangered species. PMID:25409501

  13. Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations.

    PubMed

    Koelling, V A; Hamrick, J L; Mauricio, R

    2011-02-01

    Self-fertilization is a common mating system in plants and is known to reduce genetic diversity, increase genetic structure and potentially put populations at greater risk of extinction. In this study, we measured the genetic diversity and structure of two cedar glade endemic species, Leavenworthia alabamica and L. crassa. These species have self-incompatible (SI) and self-compatible (SC) populations and are therefore ideal for understanding how the mating system affects genetic diversity and structure. We found that L. alabamica and L. crassa had high species-level genetic diversity (H(e)=0.229 and 0.183, respectively) and high genetic structure among their populations (F(ST)=0.45 and 0.36, respectively), but that mean genetic diversity was significantly lower in SC compared with SI populations (SC vs SI, H(e) for L. alabamica was 0.065 vs 0.206 and for L. crassa was 0.084 vs 0.189). We also found significant genetic structure using maximum-likelihood clustering methods. These data indicate that the loss of SI leads to the loss of genetic diversity within populations. In addition, we examined genetic distance relationships between SI and SC populations to analyze possible population history and origins of self-compatibility. We find there may have been multiple origins of self-compatibility in L. alabamica and L. crassa. However, further work is required to test this hypothesis. Finally, given their high genetic structure and that individual populations harbor unique alleles, conservation strategies seeking to maximize species-level genetic diversity for these or similar species should protect multiple populations. PMID:20485327

  14. Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

    PubMed Central

    Regidor-Cerrillo, Javier; Dez-Fuertes, Francisco; Garca-Culebras, Alicia; Moore, Dadn P.; Gonzlez-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Daz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.

    2013-01-01

    The cyst-forming protozoan parasite Neosporacaninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N. caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N. caninum, which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N. caninum-derived reference isolates from around the world and 96 N. caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N. caninum. Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N. caninum samples. Geographic sub-structuring was present in the country populations according to pairwise FST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N. caninum MLGs in cattle. PMID:23940816

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

    PubMed Central

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

    2015-01-01

    Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia. Conclusion Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman. PMID:26469349

  16. Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

    PubMed Central

    Nakajima, Yuichi; Nishikawa, Akira; Iguchi, Akira; Sakai, Kazuhiko

    2010-01-01

    Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (FST?0.033) although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained. PMID:20585399

  17. Population genetic diversity and hybrid detection in captive zebras

    PubMed Central

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

    2015-01-01

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy’s zebra E. grevyi and the mountain zebra E. zebra. The Grevy’s zebra and the mountain zebra are endangered, and hybridization between the Grevy’s zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy’s zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy’s and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy’s zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy’s zebra. PMID:26294133

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

    PubMed

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

    2015-01-01

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy's zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy's and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy's zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy's zebra. PMID:26294133

  19. 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.

  20. 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. PMID:23728203

  1. The Impact of Relationship Education on Adolescents of Diverse Backgrounds

    ERIC Educational Resources Information Center

    Adler-Baeder, Francesca; Kerpelman, Jennifer L.; Schramm, David G.; Higginbotham, Brian; Paulk, Amber

    2007-01-01

    Adolescent-focused marriage education is a relatively uncharted research area. Using a quasi-experimental design, this study examined the effectiveness of an adapted version of the curriculum entitled, "Love U2: Increasing Your Relationship Smarts" with an economically, geographically, and racially diverse sample of 340 high school students.…

  2. Structural Diversity and Close Interracial Relationships in College

    ERIC Educational Resources Information Center

    Bowman, Nicholas A.

    2012-01-01

    Recent legal and political actions have challenged the use of race-conscious college admissions policies. Earlier research offers mixed evidence about the link between an institution's racial/ethnic composition (i.e., structural diversity) and the formation of close interracial relationships, so the present study examines this topic directly for

  3. Genetic Structure of Wild Bonobo Populations: Diversity of Mitochondrial DNA and Geographical Distribution

    PubMed Central

    Higuchi, Shoko; Sakamaki, Tetsuya; Hart, John A.; Hart, Terese B.; Tokuyama, Nahoko; Reinartz, Gay E.; Guislain, Patrick; Dupain, Jef; Cobden, Amy K.; Mulavwa, Mbangi N.; Yangozene, Kumugo; Darroze, Serge; Devos, Céline; Furuichi, Takeshi

    2013-01-01

    Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species’ range. In 136 effective samples from different individuals (range: 7–37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation. PMID:23544084

  4. Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution.

    PubMed

    Kawamoto, Yoshi; Takemoto, Hiroyuki; Higuchi, Shoko; Sakamaki, Tetsuya; Hart, John A; Hart, Terese B; Tokuyama, Nahoko; Reinartz, Gay E; Guislain, Patrick; Dupain, Jef; Cobden, Amy K; Mulavwa, Mbangi N; Yangozene, Kumugo; Darroze, Serge; Devos, Céline; Furuichi, Takeshi

    2013-01-01

    Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation. PMID:23544084

  5. Comparing estimates of genetic variance across different relationship models.

    PubMed

    Legarra, Andres

    2016-02-01

    Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities". PMID:26341159

  6. Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

    PubMed Central

    Albrecht, Elena; Escobar, Miguel; Chetelat, Roger T.

    2010-01-01

    Background and Aims Two closely related, wild tomato-like nightshade species, Solanum lycopersicoides and Solanum sitiens, inhabit a small area within the Atacama Desert region of Peru and Chile. Each species possesses unique traits, including abiotic and biotic stress tolerances, and can be hybridized with cultivated tomato. Conservation and utilization of these tomato relatives would benefit from an understanding of genetic diversity and relationships within and between populations. Methods Levels of genetic diversity and population genetic structure were investigated by genotyping representative accessions of each species with a set of simple sequence repeat (SSR) and allozyme markers. Key Results As expected for self-incompatible species, populations of S. lycopersicoides and S. sitiens were relatively diverse, but contained less diversity than the wild tomato Solanum chilense, a related allogamous species native to this region. Populations of S. lycopersicoides were slightly more diverse than populations of S. sitiens according to SSRs, but the opposite trend was found with allozymes. A higher coefficient of inbreeding was noted in S. sitiens. A pattern of isolation by distance was evident in both species, consistent with the highly fragmented nature of the populations in situ. The populations of each taxon showed strong geographical structure, with evidence for three major groups, corresponding to the northern, central and southern elements of their respective distributions. Conclusions This information should be useful for optimizing regeneration strategies, for sampling of the populations for genes of interest, and for guiding future in situ conservation efforts. PMID:20154348

  7. Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis.

    PubMed

    Zhao, Yongju; Zhao, Runze; Zhao, Zhongquan; Xu, Huizhong; Zhao, Erhu; Zhang, Jiahua

    2014-06-01

    Mitochondrial DNA (mtDNA) D-loop sequences of 666 individuals (including 109 new individuals, 557 individuals retrieved from GenBank) from 33 Chinese domestic goat breeds throughout China were used to investigate their mtDNA variability and molecular phylogeography. The results showed that all goat breeds in this study proved to be extremely diverse, and the average haplotype diversity and nucleotide diversity were 0.990 ± 0.001 and 0.032 ± 0.001, respectively. The 666 sequences gave 326 different haplotypes. Phylogenetic analyses revealed that there were 4 mtDNA haplogroups identified in Chinese domestic goats, in which haplogroup A was predominant and widely distributed. Our finding was consistent with archaeological data and other genetic diversity studies. Amova analysis showed there was significant geographical structuring. Almost 84.31% of genetic variation was included in the within-breed variance component and only 4.69% was observed among the geographic distributions. This genetic diversity results further supported the previous view of multiple maternal origins of Chinese domestic goats, and the results on the phylogenetic relationship contributed to a better understanding of the history of goat domestication and modern production of domestic goats. PMID:24532161

  8. [Genetic diversity of Mongolian gazelle Procapra guttorosa Pallas, 1777].

    PubMed

    Sorokin, P A; Kiriliuk, V E; Lushchekina, A A; Kholodova, M V

    2005-10-01

    The mitochondrial DNA D-loop hypervariable fragment sequence polymorphism was examined in 27 Mongolian gazelles from Mongolia, Russia, and China. Intraspecific polymorphism of the D-loop fragment examined was demonstrated. All haplotypes described were unique. The average nucleotide diversity (pi) for the mtDNA fragment investigated constituted 5.85 +/- 2.92%. A relatively high number of insertions and deletions was observed. In particular, a haplotype with the 77-bp insertion was described. The data obtained point to high genetic diversity of Mongolian populations. There was no correlation between the distribution of haplotypes examined and geographical location of the animal tissue sampling sites. PMID:16316006

  9. Exploiting a wheat EST database to assess genetic diversity

    PubMed Central

    2010-01-01

    Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Snmez2001, and the lowest (0.622) between Aytin98 and Izgi01. PMID:21637582

  10. 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

  11. Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers

    PubMed Central

    You, Qian; Xu, Liping; Zheng, Yifeng; Que, Youxiong

    2013-01-01

    Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use. PMID:23990759

  12. Exceptionally High Levels of Genetic Diversity in Wheat Curl Mite (Acari: Eriophyidae) Populations from Turkey.

    PubMed

    Szyd?o, W; Hein, G; Denizhan, E; Skoracka, A

    2015-08-01

    Recent research on the wheat curl mite species complex has revealed extensive genetic diversity that has distinguished several genetic lineages infesting bread wheat (Triticum aestivum L.) and other cereals worldwide. Turkey is the historical region of wheat and barley (Hordeum vulgare L.) domestication and diversification. The close relationship between these grasses and the wheat curl mite provoked the question of the genetic diversity of the wheat curl mite in this region. The scope of the study was to investigate genetic differentiation within the wheat curl mite species complex on grasses in Turkey. Twenty-one wheat curl mite populations from 16 grass species from nine genera (Agropyron sp., Aegilops sp., Bromus sp., Elymus sp., Eremopyrum sp., Hordeum sp., Poa sp., Secale sp., and Triticum sp.) were sampled in eastern and southeastern Turkey for genetic analyses. Two molecular markers were amplified: the cytochrome oxidase subunit I coding region of mtDNA (COI) and the D2 region of 28S rDNA. Phylogenetic analyses revealed high genetic variation of the wheat curl mite in Turkey, primarily on Bromus and Hordeum spp., and exceptionally high diversity of populations associated with bread wheat. Three wheat-infesting wheat curl mite lineages known to occur on other continents of the world, including North and South America, Australia and Europe, were found in Turkey, and at least two new genetic lineages were discovered. These regions of Turkey exhibit rich wheat curl mite diversity on native grass species. The possible implications for further studies on the wheat curl mite are discussed. PMID:26470350

  13. Characterization and conservation of genetic diversity in subdivided populations

    PubMed Central

    Toro, M.A; Caballero, A

    2005-01-01

    We review the available tools for analysing genetic diversity in conservation programmes of subdivided populations. Ways for establishing conservation priorities have been developed in the context of livestock populations, both from the classical population genetic analysis and from the more recent Weitzman's approach. We discuss different reasons to emphasize either within or between-population variation in conservation decisions and the methodology to establish some compromise. The comparison between neutral and quantitative variation is reviewed from both theoretical and empirical points of view, and the different procedures for the dynamic management of conserved subdivided populations are discussed. PMID:16048780

  14. 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, ...

  15. 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...

  16. 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. PMID:26774060

  17. 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. PMID:22524237

  18. Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats

    PubMed Central

    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.

    2009-01-01

    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. PMID:19649327

  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. PMID:20473963

  20. Understanding Genetic Diversity and Population Structure of a Poa pratensis Worldwide Collection through Morphological, Nuclear and Chloroplast Diversity Analysis.

    PubMed

    Raggi, Lorenzo; Bitocchi, Elena; Russi, Luigi; Marconi, Gianpiero; Sharbel, Timothy F; Veronesi, Fabio; Albertini, Emidio

    2015-01-01

    Poa pratensis L. is a forage and turf grass species well adapted to a wide range of mesic to moist habitats. Due to its genome complexity little is known regarding evolution, genome composition and intraspecific phylogenetic relationships of this species. In the present study we investigated the morphological and genetic diversity of 33 P. pratensis accessions from 23 different countries using both nuclear and chloroplast molecular markers as well as flow cytometry of somatic tissues. This with the aim of shedding light on the genetic diversity and phylogenetic relationships of the collection that includes both cultivated and wild materials. Morphological characterization showed that the most relevant traits able to distinguish cultivated from wild forms were spring growth habit and leaf colour. The genome size analysis revealed high variability both within and between accessions in both wild and cultivated materials. The sequence analysis of the trnL-F chloroplast region revealed a low polymorphism level that could be the result of the complex mode of reproduction of this species. In addition, a strong reduction of chloroplast SSR variability was detected in cultivated materials, where only two alleles were conserved out of the four present in wild accessions. Contrarily, at nuclear level, high variability exist in the collection where the analysis of 11 SSR loci allowed the detection of a total of 91 different alleles. A Bayesian analysis performed on nuclear SSR data revealed that studied materials belong to two main clusters. While wild materials are equally represented in both clusters, the domesticated forms are mostly belonging to cluster P2 which is characterized by lower genetic diversity compared to the cluster P1. In the Neighbour Joining tree no clear distinction was found between accessions with the exception of those from China and Mongolia that were clearly separated from all the others. PMID:25893249

  1. Understanding Genetic Diversity and Population Structure of a Poa pratensis Worldwide Collection through Morphological, Nuclear and Chloroplast Diversity Analysis

    PubMed Central

    Russi, Luigi; Marconi, Gianpiero; Sharbel, Timothy F.; Veronesi, Fabio; Albertini, Emidio

    2015-01-01

    Poa pratensis L. is a forage and turf grass species well adapted to a wide range of mesic to moist habitats. Due to its genome complexity little is known regarding evolution, genome composition and intraspecific phylogenetic relationships of this species. In the present study we investigated the morphological and genetic diversity of 33 P. pratensis accessions from 23 different countries using both nuclear and chloroplast molecular markers as well as flow cytometry of somatic tissues. This with the aim of shedding light on the genetic diversity and phylogenetic relationships of the collection that includes both cultivated and wild materials. Morphological characterization showed that the most relevant traits able to distinguish cultivated from wild forms were spring growth habit and leaf colour. The genome size analysis revealed high variability both within and between accessions in both wild and cultivated materials. The sequence analysis of the trnL-F chloroplast region revealed a low polymorphism level that could be the result of the complex mode of reproduction of this species. In addition, a strong reduction of chloroplast SSR variability was detected in cultivated materials, where only two alleles were conserved out of the four present in wild accessions. Contrarily, at nuclear level, high variability exist in the collection where the analysis of 11 SSR loci allowed the detection of a total of 91 different alleles. A Bayesian analysis performed on nuclear SSR data revealed that studied materials belong to two main clusters. While wild materials are equally represented in both clusters, the domesticated forms are mostly belonging to cluster P2 which is characterized by lower genetic diversity compared to the cluster P1. In the Neighbour Joining tree no clear distinction was found between accessions with the exception of those from China and Mongolia that were clearly separated from all the others. PMID:25893249

  2. [Discoverer of genetic principle for antibody diversity--Susumu Tonegawa].

    PubMed

    Guo, Xiao-Qiang

    2012-11-01

    Susumu Tonegawa is a Japanese molecular biologist who won the Nobel Prize for Physiology or Medicine in 1987 for his discovery of "the genetic principle for generation of antibody diversity". Susumu Tonegawa is also famous for his important contributions on neuroscience, who explored the molecular and cellular mechanisms underlying learning and memory. In this article, the life and research on Susumu Tonegawa was introduced. PMID:23208148

  3. Genetic diversity of Plasmodium vivax malaria in China and Myanmar

    PubMed Central

    Zhong, Daibin; Bonizzoni, Mariangela; Zhou, Guofa; Wang, Guangze; Chen, Bin; Vardo-Zalik, Anne; Cui, Liwang; Yan, Guiyun; Zheng, Bin

    2011-01-01

    Genetic diversity and population structure of Plasmodium vivax parasites are valuable to the prediction of the origin and spread of novel variants within and between populations, and to the program evaluation of malaria control measures. Using two polymorphic genetic markers, the merozoite surface protein genes PvMSP-3? and PvMSP-3?, we investigated the genetic diversity of four Southeast Asian P. vivax populations, representing both subtropical and temperate strains with dramatically divergent relapse patterns. PCR amplification of PvMSP-3? and PvMSP-3? genes detected three and four major size polymorphisms among the 235 infections examined, respectively, while restriction analysis detected 15 and 19 alleles, respectively. Samples from different geographical areas differed dramatically in their PvMSP-3? and PvMSP-3? allele composition and frequency. Samples tended to cluster on the basis of their PCR-RFLP polymorphism. These results indicated that different parasite genotypes were circulating in each endemic area, and that geographic isolation may exist. Multiple infections were detected in all four parasite populations, ranging from 20.5% to 31.8%, strongly indicating that P. vivax populations were highly diverse and multiple clonal infections are common in these malaria-hypoendemic regions of Southeast Asia. PMID:21624503

  4. Genetic diversity of Plasmodium vivax in Kolkata, India

    PubMed Central

    Kim, Jung-Ryong; Imwong, Mallika; Nandy, Amitabha; Chotivanich, Kesinee; Nontprasert, Apichart; Tonomsing, Naowarat; Maji, Ardhendu; Addy, Manjulika; Day, Nick PJ; White, Nicholas J; Pukrittayakamee, Sasithon

    2006-01-01

    Background Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains. Methods Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs), the merozoite surface protein 1 (pvmsp1) and the merozoite surface protein 3-alpha (pvmsp3-alpha). Results Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp1 and 37 for pvmsp3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151). The overall rate of mixed genotype infections was 10.6%. Conclusion These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria. PMID:16907979

  5. Genetic diversity and population structure of Salvia miltiorrhiza Bge in China revealed by ISSR and SRAP.

    PubMed

    Song, Zhenqiao; Li, Xingfeng; Wang, Honggang; Wang, Jianhua

    2010-02-01

    Salvia miltiorrhiza Bge is a traditional Chinese medicinal herb used as an important drug to cure cardiovascular diseases. In this work, inter simple sequence repeats (ISSR) and sequence related amplified polymorphism (SRAP) markers, were applied to assess the level and pattern of genetic diversity in five important cultivated populations of S. miltiorrhiza. Among these populations, 120 bands were amplified by 5 ISSR primers, of which all were polymorphic, and 110 polymorphic bands (90.16%) were observed in 122 bands amplified by 6 SRAP primers. A high levels of genetic diversity at the species level was detected with Hs = 0.1951, 0.1927 respectively. Analysis of molecular variance revealed that a greater proportion of total genetic variation existed within populations (86.64 and 84.83% respectively) rather than among populations (13.36 and 15.17% respectively). Cluster analysis divided the five populations into two groups. The genetic relationships among populations have low correlation with their geographical distribution (Mantel test; r = 0.4870 and 0.5740 respectively). The study indicated that both ISSR and SRAP markers were effective and reliable for assessing the degree of genetic variation of S. miltiorrhiza. Our results suggested that random collecting, preserving and planting seeds without deliberate selection might be an efficient way to conserve genetic resources of medicinal plants. Their effective use was also discussed on the further breeding. PMID:19844793

  6. Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum).

    PubMed

    Badigannavar, Ashok; Myers, Gerald O

    2015-03-01

    Cottonseed contains 16% seed oil and 23% seed protein by weight. High levels of palmitic acid provides a degree of stability to the oil, while the presence of bound gossypol in proteins considerably changes their properties, including their biological value. This study uses genetic principles to identify genomic regions associated with seed oil, protein and fibre content in upland cotton cultivars. Cotton association mapping panel representing the US germplasm were genotyped using amplified fragment length polymorphism markers, yielding 234 polymorphic DNA fragments. Phenotypic analysis showed high genetic variability for the seed traits, seed oil range from 6.47-25.16%, protein from 1.85-28.45% and fibre content from 15.88-37.12%. There were negative correlations between seed oil and protein content.With reference to genetic diversity, the average estimate of FST was 8.852 indicating a low level of genetic differentiation among subpopulations. The AMOVA test revealed that variation was 94% within and 6% among subpopulations. Bayesian population structure identified five subpopulations and was in agreement with their geographical distribution. Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic relationships and their utilization in breeding programmes. PMID:25846880

  7. Evaluation of bamboo genetic diversity using morphological and SRAP analyses.

    PubMed

    Zhu, S; Liu, T; Tang, Q; Fu, L; Tang, Sh

    2014-03-01

    Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections. PMID:25438551

  8. Evaluation of bamboo genetic diversity using morphological and SRAP analyses.

    PubMed

    Zhu, S; Liu, T; Tang, Q; Fu, L; Tang, Sh

    2014-03-01

    Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections. PMID:25508082

  9. Genetic diversity and population structure in wild Sichuan rhesus macaques.

    PubMed

    Li, Di Yan; Xu, Huai Liang; Trask, Jessica Satkoski; Zhu, Qing; Cheng, An Chun; Smith, David Glenn; George, Debbie; Zhang, Long

    2013-04-01

    Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy-Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity. PMID:23269618

  10. 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.

  11. 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

  12. 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

  13. 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. PMID:25333358

  14. Genetic diversity of locally adapted sheep from Pantanal region of Mato Grosso do Sul.

    PubMed

    Crispim, B A; Grisolia, A B; Seno, L O; Egito, A A; Vargas Junior, F M; Souza, M R

    2013-01-01

    Sheep of the Pantaneiro breed and seven other breeds, raised in the State of Mato Grosso do Sul, Brazil, were genotyped using eight microsatellite loci. The aim of the present study was to determine the genetic variability, phylogenetic relationship, and patterns of gene introgression and miscegenation among the animals surveyed, to obtain information about the genetic structure of locally adapted sheep in Mato Grosso do Sul. A total of 195 animals were used for genetic analysis. The Pantaneiro breed had the largest average number of alleles/locus (9.25), and higher allelic richness (6.95), while the Dorper population had the lowest values for these parameters (4.88 and 3.86, respectively). Analysis of genetic distance values and genetic structure between populations made it possible to characterize these animals with regard to distinct genetic groups. Average expected heterozygosity ranged from 0.72 (Pantaneiro) to 0.55 (Dorper), while average observed heterozygosity ranged from 0.63 (White Dorper) to 0.54 (Dorper). On the basis of the statistical parameters evaluated, it was possible to demonstrate that when compared to other populations, the Pantaneiro breed represented a reservoir of genetic diversity with rare and useful alleles for genetic improvement, emphasizing the importance of preserving the breed. PMID:24301918

  15. Genetic diversity and the genetic structure of natural populations of Chamaecyparis obtusa: implications for management and conservation.

    PubMed

    Tsumura, Y; Matsumoto, A; Tani, N; Ujino-Ihara, T; Kado, T; Iwata, H; Uchida, K

    2007-08-01

    We investigated 25 natural populations of Chamaecyparis obtusa using 51 cleaved amplified polymorphic sequence (CAPS) markers, which were developed using information on sequence-tagged sites (STS) in Cryptomeria japonica. Most CAPS markers have codominant expression patterns, and are suitable for population studies because of their robustness and convenience. We estimated various genetic diversity parameters, including average heterozygosity (H(e)) and allelic richness and found that the more peripheral populations tended to have lower genetic diversity than central populations, in agreement with a previous theoretical study. The overall genetic differentiation between populations was low, but statistically significant (G(ST)=0.039), and similar to the level reported in a previous allozyme study. We attempted to detect non-neutral loci associated with local adaptation to clarify the relationship between the fixation index (F(ST)) and H(e) values for each locus and found seven candidates non-neutral loci. Phylogenetic tree analysis of the populations and Bayesian clustering analysis revealed a pattern of gradually increasing isolation of populations with increasing geographical distance. Three populations had a high degree of linkage disequilibrium, which we attribute to severe bottlenecks due to human disturbance or competition with other species during their migration from refugia after the most recent glaciation. We concluded that the small populations in western Japan and in Kanto district are more important, from a conservation perspective, than the populations in central Japan, due to their genetic divergence, relatively small sizes and restricted areas. PMID:17473864

  16. [Genetic relationship and parent selection of some Sarcandra glabra resources based on ISSR].

    PubMed

    Wei, Yi-Cong; Chen, Ying; Luo, Lin-Quan; Yang, Qun-Xiong; Chen, Yi-Juan; Liang, Yi-Chi

    2014-12-01

    The study is aimed to assess the genetic diversity and genetic relationship of 18 Sarcandra glabra resources from different populations,and guide parent selection of cross breeding between these resources. The molecular marker technique ISSR was used to investigate the genetic diversity of the 18 resources. Data was analyzed by POPGEN 32, and a cluster diagram was presented by UPGMA. One hundred and ninety-eight amplified fragments were obtained using 23 ISSR primers. One hundred and eighty-four polymorphic loci were identified. Nei's genetic diversity index (h) was 0.32, Shannon diversity index (I) was 0.485 4. The genetic similarity coefficient among the resources ranged from 0.383 8 to 0.878 8 in an average of 0.661 2. The genetic distance between sample S2 and sample S18 was the farthest, so as between sample S3 and sample S18 both Nei's genetic distance was 0.957 5, The genetic distance between sample S4 and sample S5 was the closest, the Nei's genetic distance was 0.129 2,and the sample S1, S2, S3, S7, S10 were significantly different from the others based on the clustering analysis, the three groups S2 vs S3, S2 vs S6, S2 vs S18 were the best parent group selection. There was a middle level of genetic differentiation in the resources. The genetic distance between resources gives useful information to guide parent selection of cross breeding. PMID:25911803

  17. Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds.

    PubMed

    Bmcke, Elisabeth; Gengler, Nicolas; Cothran, E Gus

    2011-01-01

    In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever. PMID:21637546

  18. 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...

  19. Genetic differentiation and diversity of Callosobruchus chinensis collections from China.

    PubMed

    Duan, C X; Li, W C; Zhu, Z D; Li, D D; Sun, S L; Wang, X M

    2016-02-01

    Callosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0-47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191-0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (F ST ) values ranged from 0.049 to 0.441 with a total F ST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster. PMID:26548842

  20. 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...

  1. Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity

    PubMed Central

    2012-01-01

    Background Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds. Methods For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach. Results Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank. Conclusions A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program. PMID:22620856

  2. Prevalence and genetic diversity of arcobacter in food products in the north of Spain.

    PubMed

    Nieva-Echevarria, Barbara; Martinez-Malaxetxebarria, Irati; Girbau, Cecilia; Alonso, Rodrigo; Fernández-Astorga, Aurora

    2013-08-01

    The bacterial contamination of food products can cause serious public health problems. Interest in Arcobacter contamination has increased due to the relationship between these bacteria and human enteritis. We studied the prevalence and genetic diversity of Arcobacter species at the retail level in the province of Alava in Basque Country, Spain. The results showed a high genetic diversity and indicated the regular presence of the main Arcobacter spp. associated with human enteric illness in food products. Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii were detected with an overall prevalence close to 40% and were isolated from 15 (42.8%) fresh cow's milk samples, 12 (73.3%) shellfish samples, 11 (55%) chicken samples, 2 (10%) pork samples, and 1 (5%) beef sample. The results indicate the need to investigate the impact of Arcobacter spp. on public health. PMID:23905804

  3. Using Plant Functional Traits to Explain DiversityProductivity Relationships

    PubMed Central

    Roscher, Christiane; Schumacher, Jens; Gubsch, Marln; Lipowsky, Annett; Weigelt, Alexandra; Buchmann, Nina; Schmid, Bernhard; Schulze, Ernst-Detlef

    2012-01-01

    Background The different hypotheses proposed to explain positive species richnessproductivity relationships, i.e. selection effect and complementarity effect, imply that plant functional characteristics are at the core of a mechanistic understanding of biodiversity effects. Methodology/Principal Findings We used two community-wide measures of plant functional composition, (1) community-weighted means of trait values (CWM) and (2) functional trait diversity based on Raos quadratic diversity (FDQ) to predict biomass production and measures of biodiversity effects in experimental grasslands (Jena Experiment) with different species richness (2, 4, 8, 16 and 60) and different functional group number and composition (1 to 4; legumes, grasses, small herbs, tall herbs) four years after establishment. Functional trait composition had a larger predictive power for community biomass and measures of biodiversitity effects (4082% of explained variation) than species richness per se (<113% of explained variation). CWM explained a larger amount of variation in community biomass (80%) and net biodiversity effects (70%) than FDQ (36 and 38% of explained variation respectively). FDQ explained similar proportions of variation in complementarity effects (24%, positive relationship) and selection effects (28%, negative relationship) as CWM (27% of explained variation for both complementarity and selection effects), but for all response variables the combination of CWM and FDQ led to significant model improvement compared to a separate consideration of different components of functional trait composition. Effects of FDQ were mainly attributable to diversity in nutrient acquisition and life-history strategies. The large spectrum of traits contributing to positive effects of CWM on biomass production and net biodiversity effects indicated that effects of dominant species were associated with different trait combinations. Conclusions/Significance Our results suggest that the identification of relevant traits and the relative impacts of functional identity of dominant species and functional diversity are essential for a mechanistic understanding of the role of plant diversity for ecosystem processes such as aboveground biomass production. PMID:22623961

  4. Analysis of genetic diversity among Chinese wild Vitis species revealed with SSR and SRAP markers.

    PubMed

    Jing, Z B; Wang, X P; Cheng, J M

    2013-01-01

    The genetic diversity among 80 Vitis materials including 62 indigenous accessions of 17 wild Vitis species in China and 7 interspecific hybrids, 10 V. vinifera L. cultivars, and 1 V. riparia Michaux were evaluated by simple sequence repeat and sequence-related amplified polymorphism markers. A total of 10 simple sequence repeat primers and 11 sequence-related amplified polymorphism primer combinations were amplified, and 260 bands were generated, of which 252 were polymorphic with an average polymorphism rate of 97.02%. Genetic relationships among the different Vitis species indicated that V. ficifolia and V. yeshanensis could be considered a separate species. As for the 4 major ecogeographic regions of Chinese wild Vitis species, the genetic diversities of Chinese wild Vitis species from the Qinling Mountain region (H = 0.1947, I = 0.3067) and the mid-downstream Yangtze River region (H = 0.1834, I = 0.2925) were higher, with results suggesting that these regions may be one of the major centers of Vitis origin. An understanding of the genetic diversity of these Chinese wild Vitis species could provide the theoretical foundation for further protection and reasonable utilization in grape breeding. PMID:23913379

  5. Genetic diversity of Qatari date palm using SSR markers.

    PubMed

    Elmeer, K; Mattat, I

    2015-01-01

    The genetic diversity in the date palm germplasm of 59 female accessions representing 12 cultivars from different locations in Qatar was investigated using 14 loci of simple-sequence repeat (SSR) primers. A total of 94 alleles, with a mean of 6.7 alleles per locus, were scored. The number of alleles per locus varied from 3 (primer mPdCIR090) to 11 (primers mPdCIR010 and mPdCIR015). The amplified SSR band sizes ranged from 104 to 330 bp. The mean gene diversity was 0.66 and ranged from 0.39 (locus mPdCIRO93) to 0.86 (locus mPdCIR015), indicating that the Qatari date palm collection has a high degree of genetic diversity. The heterozygosity ranged from 0 (marker mPdCIR090) to 98% (marker mPdCIR010). Forty-four percent of the variability is explained at the inter-population level, while 56% of the variability is maintained within individuals. However, the loci mPdCIR044, mPdCIR057, mPdCIR090, and mPdCIR093 revealed that the total gene diversity is explained at the inter-population level. The Qatari populations Khalas, Shishi, Barhi, Hillali, Khnaizi, Gar, and Jabri showed significant differentiation compared to all other populations. The average fixation index was 0.24814, showing that about 24.81% of the genetic variation was present among populations, which correlated with analysis of molecular variance. PMID:25867305

  6. 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

  7. Genetic diversity and bottleneck studies in the Marwari horse breed.

    PubMed

    Gupta, A K; Chauhan, M; Tandon, S N

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (-/+ s.e.) allelic diversity was 5.9 (-/+ 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (-/+ s.e.) effective number of alleles (3.3 -/+ 1.27), observed heterozygosity (0.5306 -/+ 0.22), expected Levene's heterozygosity (0.6612 -/+ 0.15), expected Nei's heterozygosity (0.6535 -/+ 0.14), and polymorphism information content (0.6120 -/+ 0.03). Low values of Wright's fixation index, F(IS) (0.2433 -/+ 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal 'L' shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant M ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers. PMID:16385161

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

    PubMed

    Gibb, Heloise; Johansson, Therese; Stenbacka, Fredrik; Hjltn, 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

  9. 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

  10. Genetic basis of transcriptome diversity in Drosophila melanogaster.

    PubMed

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M; Peiffer, Jason A; Lyman, Richard F; Stone, Eric A; Anholt, Robert R H; Mackay, Trudy F C

    2015-11-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

  11. Genetic basis of transcriptome diversity in Drosophila melanogaster

    PubMed Central

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M.; Peiffer, Jason A.; Lyman, Richard F.; Stone, Eric A.; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

  12. Genetic relationships among cherry species with transferability of simple sequence repeat loci.

    PubMed

    Khadivi-Khub, Abdollah

    2014-09-01

    Sweet and sour cherries are two economically important species in the world. The capability to distinguish among cherry genotypes in breeding, cultivation and germplasm collection is extremely important for scientific as well as economic reasons. In the present research, sixteen simple sequences repeat (SSR) loci were used to estimate the relationships among sweet, sour, duke and wild cherries. All of the SSR markers showed high transferability across the studied species that allowed us to study genetic diversity in them. Totally 96 alleles were generated with SSR loci, of which 93 were found polymorphic with 97.57 % polymorphism. Values of genetic similarity between genotypes varied from 0.16 to 0.97 which indicated high level of genetic diversity. On the basis of their genetic similarities, SSR analysis allowed to group the genotypes into three main clusters according to their species. These results have an important implication for cherry germplasm characterization, improvement, and conservation. PMID:24973884

  13. Peach genetic resources: diversity, population structure and linkage disequilibrium

    PubMed Central

    2013-01-01

    Background Peach (Prunus persica (L.) Batsch) is one of the most important model fruits in the Rosaceae family. Native to the west of China, where peach has been domesticated for more than 4,000 years, its cultivation spread from China to Persia, Mediterranean countries and to America. Chinese peach has had a major impact on international peach breeding programs due to its high genetic diversity. In this research, we used 48 highly polymorphic SSRs, distributed over the peach genome, to investigate the difference in genetic diversity, and linkage disequilibrium (LD) among Chinese cultivars, and North American and European cultivars, and the evolution of current peach cultivars. Results In total, 588 alleles were obtained with 48 SSRs on 653 peach accessions, giving an average of 12.25 alleles per locus. In general, the average value of observed heterozygosity (0.47) was lower than the expected heterozygosity (0.60). The separate analysis of groups of accessions according to their origin or reproductive strategies showed greater variability in Oriental cultivars, mainly due to the high level of heterozygosity in Chinese landraces. Genetic distance analysis clustered the cultivars into two main groups: one included four wild related Prunus, and the other included most of the Oriental and Occidental landraces and breeding cultivars. STRUCTURE analysis assigned 469 accessions to three subpopulations: Oriental (234), Occidental (174), and Landraces (61). Nested STRUCTURE analysis divided the Oriental subpopulation into two different subpopulations: ‘Yu Lu’ and ‘Hakuho’. The Occidental breeding subpopulation was also subdivided into nectarine and peach subpopulations. Linkage disequilibrium (LD) analysis in each of these subpopulations showed that the percentage of linked (r2 > 0.1) intra-chromosome comparisons ranged between 14% and 47%. LD decayed faster in Oriental (1,196 Kbp) than in Occidental (2,687 Kbp) samples. In the ‘Yu Lu’ subpopulation there was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. Conclusions Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach. PMID:24041442

  14. Diversity and Phylogenetic Relationships among the North American Tacaribe Serocomplex Viruses (Family Arenaviridae)

    PubMed Central

    Cajimat, Maria N. B.; Milazzo, Mary Louise; Haynie, Michelle L.; Hanson, J. Delton; Bradley, Robert D.; Fulhorst, Charles F.

    2011-01-01

    The purpose of this study was to extend our knowledge of the genetic diversity and phylogenetic relationships among the North American Tacaribe serocomplex viruses. Analyses of glycoprotein precursor gene sequence data separated the North American arenaviruses into 7 major phylogenetic groups. The results of analyses of Z gene and nucleocapsid protein gene sequence data were not remarkably different from the glycoprotein precursor gene tree. In contrast, the tree generated from RNA-dependent RNA polymerase gene sequences differed from the glycoprotein precursor gene tree with regard to phylogenetic relationships among the viruses associated with woodrats captured in the western United States, Texas, or northern Mexico. Further analyses of the polymerase gene sequence data set suggested that the difference in topology was a consequence of incongruence among the gene tree data sets or chance rather than genetic reassortment or recombination between arenaviruses. PMID:21982818

  15. 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. PMID:22530022

  16. 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

  17. Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae).

    PubMed

    Ferreira, L F R; Duarte, K M R; Gomes, L H; Carvalho, R S; Leal Junior, G A; Aguiar, M M; Armas, R D; Tavares, F C A

    2012-01-01

    The causal agent of witches' broom disease, Moniliophthora perniciosa is a hemibiotrophic and endemic fungus of the Amazon basin and the most important cocoa disease in Brazil. The purpose of this study was to analyze the genetic diversity of polysporic isolates of M. perniciosa to evaluate the adaptation of the pathogen from different Brazilian regions and its association with different hosts. Polysporic isolates obtained previously in potato dextrose agar cultures of M. perniciosa from different Brazilian states and different hosts (Theobroma cacao, Solanum cernuum, S. paniculatum, S. lycocarpum, Solanum sp, and others) were analyzed by somatic compatibility grouping where the mycelium interactions were distinguished after 4-8 weeks of confrontation between the different isolates of M. perniciosa based on the precipitation line in the transition zone and by protein electrophoresis through SDS-PAGE. The diversity of polysporic isolates of M. perniciosa was grouped according to geographic proximity and respective hosts. The great genetic diversity of M. perniciosa strains from different Brazilian states and hosts favored adaptation in unusual environments and dissemination at long distances generating new biotypes. PMID:22869076

  18. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    PubMed Central

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajimas D and Fu and Lis F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  19. 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

  20. LYGUS GENETICS: INTER- AND INTRASPECIFIC MITOCHONDRIAL GENETIC DIVERSITY IN NORTH AMERICA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondrial DNA (mtDNA) was employed to investigate inter- and intraspecific genetic diversity within the Lygus genus. The main emphasis was on L. lineolaris because it is a widely dispersed species occurring in many regions of North America. Part of the mtDNA cox1 and cox2 gene regions were used ...

  1. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    PubMed Central

    Seo, Dongwon; Bhuiyan, Md. Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-01-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  2. [Genetic diversity of a germplasm collection of Cucumis melo L. using SRAP markers].

    PubMed

    Chen, Yun; Li, Guan; Wang, Xian Lei

    2010-07-01

    Genetic relationships and classifications of a set of melon accessions were analyzed to provide the experimental support for utilizing effectively genetic materials for breeding. Sequence-related amplified polymorphism technique was adopted to analyze 61 melon accessions. Sixteen primer combinations with clear band pattern and polymorphism were selected from over 42 primer combinations. Four hundred and fifty-two loci were detected by 16 pairs of SRAP primers. Among them, 265 were polymorphic, the polymorphic rate was 58.63%, and 28.56 loci and 16.56 polymorphic loci were amplified by each pairs of primers on average. The genetic similarity coefficient of the 61 accessions ranged from 0.48 to 0.93, with an average of 0.73. These results suggested that there was rich genetic diversity among the melon accessions tested. The varieties examined were clustered into two groups,which were thick-skinned melon and thin-skinned melon. Five groups were clustered according to genetic similarity coefficient of 0.74. The Nei's gene diversity index and Shannon's Information index of melon were 0.2231 and 0.3422, respectively, in Xinjiang, the highest among all the ecological regions. PMID:20650857

  3. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  4. 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 identification of varieties or cultivars, and also for genome mapping in tef. PMID:15061798

  5. Genetic diversity among Lagenaria siceraria accessions containing resistance to root-knot nematodes, whiteflies, ZYMV or powdery mildew

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In recent years, there has been an increased interest in Europe and in the U.S. in grafting watermelon onto bottle gourd, Lagenaria siceraria (Mol.) Standl. In this study, genetic diversity and relationships were examined [using 240 sequence related amplified polymorphism (SRAP) markers] among 56 U...

  6. Bioinformatics analysis and genetic diversity of the poliovirus.

    PubMed

    Liu, Yanhan; Ma, Tengfei; Liu, Jianzhu; Zhao, Xiaona; Cheng, Ziqiang; Guo, Huijun; Wang, Shujing; Xu, Ruixue

    2014-12-01

    Poliomyelitis, a disease which can manifest as muscle paralysis, is caused by the poliovirus, which is a human enterovirus and member of the family Picornaviridae that usually transmits by the faecal-oral route. The viruses of the OPV (oral poliovirus attenuated-live vaccine) strains can mutate in the human intestine during replication and some of these mutations can lead to the recovery of serious neurovirulence. Informatics research of the poliovirus genome can be used to explain further the characteristics of this virus. In this study, sequences from 100 poliovirus isolates were acquired from GenBank. To determine the evolutionary relationship between the strains, we compared and analysed the sequences of the complete poliovirus genome and the VP1 region. The reconstructed phylogenetic trees for the complete sequences and the VP1 sequences were both divided into two branches, indicating that the genetic relationships of the whole poliovirus genome and the VP1 sequences are very similar. This branching indicates that the virulence and pathogenicity of poliomyelitis may be associated with the VP1 region. Sequence alignment of the VP1 region revealed numerous mutation sites in which mutation rates of >30?% were detected. In a group of strains recorded in the USA, mutation sites and mutation types were the same and this may be associated with their distribution in the evolutionary tree and their genetic relationship. In conclusion, the genetic evolutionary relationships of poliovirus isolate sequences are determined to a great extent by the VP1 protein, and poliovirus strains located on the same branch of the phylogenetic tree contain the same mutation spots and mutation types. Hence, the genetic characteristics of the VP1 region in the poliovirus genome should be analysed to identify the transmission route of poliovirus and provide the basis of viral immunity development. PMID:25261065

  7. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-01-01

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters. PMID:26345904

  8. [Analysis of genetic diversity of population of Northern Eurasia from autosomal microsatellite loci].

    PubMed

    Stepanov, V A; Spiridonova, M G; Tadinova, V N; Puzyrev, V P

    2003-10-01

    The paper presents the results of analysis of the gene pools of several North Eurasian ethnic groups (Buryats, Evenks, Altaians, Russians, Kyrgyzes, Tuvinians, Tatars, and Ukrainians) examined using a panel of autosomal microsatellite markers (D4S397, D5S393, D7S640, D8S514, D9S161, D10S197, D11S1358, D12S364, and D13S173) mapped on different chromosomes and represented by the (CA)n dinucleotide repeats. In the group of populations examined the proportion of genetic variability at microsatellite loci explained by interpopulation differences was about 2.5%, while genetic differences between the individuals within a population accounted for 97.5% of this variability. Analysis of genetic relationships among the populations revealed substantial differences between the populations belonging to the Indo-European and Altaic linguistic families in gene diversity at microsatellite loci. PMID:14658343

  9. Multiple Mating But Not Recombination Causes Quantitative Increase in Offspring Genetic Diversity for Varying Genetic Architectures

    PubMed Central

    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. PMID:23077571

  10. Host Range, Prevalence, and Genetic Diversity of Adenoviruses in Bats?

    PubMed Central

    Li, Yan; Ge, Xingyi; Zhang, Huajun; Zhou, Peng; Zhu, Yan; Zhang, Yunzhi; Yuan, Junfa; Wang, Lin-Fa; Shi, Zhengli

    2010-01-01

    Bats are the second largest group of mammals on earth and act as reservoirs of many emerging viruses. In this study, a novel bat adenovirus (AdV) (BtAdV-TJM) was isolated from bat fecal samples by using a bat primary kidney cell line. Infection studies indicated that most animal and human cell lines are susceptible to BtAdV-TJM, suggesting a possible wide host range. Genome analysis revealed 30 putative genes encoding proteins homologous to their counterparts in most known AdVs. Phylogenetic analysis placed BtAdV-TJM within the genus Mastadenovirus, most closely related to tree shrew and canine AdVs. PCR analysis of 350 bat fecal samples, collected from 19 species in five Chinese provinces during 2007 and 2008, indicated that 28 (or 8%) samples were positive for AdVs. The samples were from five bat species, Hipposideros armiger, Myotis horsfieldii, M. ricketti, Myotis spp., and Scotophilus kuhlii. The prevalence ranged from 6.25% (H. armiger in 2007) to 40% (M. ricketti in 2007). Comparison studies based on available partial sequences of the pol gene demonstrated a great genetic diversity among bat AdVs infecting different bat species as well as those infecting the same bat species. This is the first report of a genetically diverse group of DNA viruses in bats. Our results support the notion, derived from previous studies based on RNA viruses (especially coronaviruses and astroviruses), that bats seem to have the unusual ability to harbor a large number of genetically diverse viruses within a geographic location and/or within a taxonomic group. PMID:20089640

  11. Racially and ethnically diverse schools and adolescent romantic relationships.

    PubMed

    Strully, Kate

    2014-11-01

    Focusing on romantic relationships, which are often seen as a barometer of social distance, this analysis investigates how adolescents from different racial-ethnic and gender groups respond when they attend diverse schools with many opportunities for inter-racial-ethnic dating. Which groups respond by forming inter-racial-ethnic relationships, and which groups appear to "work around" opportunities for inter-racial-ethnic dating by forming more same-race-ethnicity relationships outside of school boundaries? Most prior studies have analyzed only relationships within schools and, therefore, cannot capture a potentially important way that adolescents express preferences for same-race-ethnicity relationships or work around constraints from other groups' preferences. Using the National Longitudinal Study of Adolescent Health, I find that, when adolescents are in schools with many opportunities for inter-racial-ethnic dating, black females and white males are most likely to form same-race-ethnicity relationships outside of the school; whereas Hispanic males and females are most likely to date across racial-ethnic boundaries within the school. PMID:25848670

  12. Racially and Ethnically Diverse Schools and Adolescent Romantic Relationships*

    PubMed Central

    Strully, Kate

    2015-01-01

    Focusing on romantic relationships, which are often seen as a barometer of social distance, this analysis investigates how adolescents from different racial-ethnic and gender groups respond when they attend diverse schools with many opportunities for inter-racial-ethnic dating. Which groups respond by forming inter-racial-ethnic relationships, and which groups appear to “work around” opportunities for inter-racial-ethnic dating by forming more same-race-ethnicity relationships outside of school boundaries? Most prior studies have analyzed only relationships within schools and, therefore, cannot capture a potentially important way that adolescents express preferences for same-race-ethnicity relationships and/or work around constraints from other groups’ preferences. Using the National Longitudinal Study of Adolescent Health, I find that, when adolescents are in schools with many opportunities for inter-racial-ethnic dating, black females and white males are most likely to form same-race-ethnicity relationships outside of the school; whereas Hispanic males and females are most likely to date across racial-ethnic boundaries within the school. PMID:25848670

  13. Genetics, genomics and evolution of ergot alkaloid diversity.

    PubMed

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

    2015-04-01

    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

  14. 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

  15. 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. PMID:25917305

  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. Ethnic diversity in the genetics of venous thromboembolism.

    PubMed

    Tang, Liang; Hu, Yu

    2015-11-01

    Genetic susceptibility is considered as a crucial factor for the development of venous thromboembolism (VTE). Epidemiologic and genetic studies have revealed clear disparities in the incidence of VTE and the distribution of genetic factors for VTE in populations stratified by ethnicity worldwide. While gain-of-function polymorphisms in the procoagulant genes are common inherited factors in European-origin populations, the most prevalent molecular basis for venous thrombosis in Asians is confirmed to be dysfunctional variants in the anticoagulant genes. With the breakthrough of genomic technologies, a set of novel common alleles and rare mutations associated with VTE have also been identified, in different ethnic groups. Several putative pathways contributing to the pathogenesis of thrombophilia in populations of African-ancestry are largely unknown, as current knowledge of hereditary and acquired risk factors do not fully explain the highest risk of VTE in Black groups. In-depth studies across diverse ethnic populations are needed to unravel the whole genetics of VTE, which will help developing individual risk prediction models and strategies to minimise VTE in all populations. PMID:26156046

  18. Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae).

    PubMed

    Alves, M F; Barroso, P A V; Ciampi, A Y; Hoffmann, L V; Azevedo, V C R; Cavalcante, U

    2013-01-01

    Gossypium mustelinum is the only cotton species native to Brazil; it is endemic to the semi-arid region of the northeast. The populations are found near perennial and semi-perennial sources of water, such as ponds or pools in intermittent streams. Problems with in situ conservation derive from human interference in its habitat, mainly because of excessive cattle grazing and deforestation. Establishing efficient strategies for in situ conservation requires knowledge of the genetic structure of the populations. We evaluated the structure and genetic variability of populations of G. mustelinum in the Toc and Capivara Rivers (State of Bahia). Two hundred and eighteen mature G. mustelinum plants were genotyped with SSR markers. The molecular data were used to estimate the allelic frequencies, the heterozygosity, the F statistics, and the genetic distance among the populations and among individuals. We found high genetic diversity among the populations. The FST indexes for each population were also high and strongly correlated with physical distance. The high estimated level of endogamy and the low observed heterozygosity are indicative that the populations reproduce mainly by self-fertilization and crosses between related individuals. Consequently, strategies for in situ preservation should include at least three occurrence sites of G. mustelinum from each population. For ex situ conservation, the collections should include as many sites as possible. PMID:23512677

  19. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    PubMed Central

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use. PMID:23497049

  20. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi

    PubMed Central

    He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

    2015-01-01

    Background Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. Methods This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. Discussion The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement. PMID:26317414

  1. Genetic variation in the Sorbs of eastern Germany in the context of broader European genetic diversity

    PubMed Central

    Veeramah, Krishna R; Tnjes, Anke; Kovacs, Peter; Gross, Arnd; Wegmann, Daniel; Geary, Patrick; Gasperikova, Daniela; Klimes, Iwar; Scholz, Markus; Novembre, John; Stumvoll, Michael

    2011-01-01

    Population isolates have long been of interest to genetic epidemiologists because of their potential to increase power to detect disease-causing genetic variants. The Sorbs of Germany are considered as cultural and linguistic isolates and have recently been the focus of disease association mapping efforts. They are thought to have settled in their present location in eastern Germany after a westward migration from a largely Slavic-speaking territory during the Middle Ages. To examine Sorbian genetic diversity within the context of other European populations, we analyzed genotype data for over 30?000 autosomal single-nucleotide polymorphisms from over 200 Sorbs individuals. We compare the Sorbs with other European individuals, including samples from population isolates. Despite their geographical proximity to German speakers, the Sorbs showed greatest genetic similarity to Polish and Czech individuals, consistent with the linguistic proximity of Sorbian to other West Slavic languages. The Sorbs also showed evidence of subtle levels of genetic isolation in comparison with samples from non-isolated European populations. The level of genetic isolation was less than that observed for the Sardinians and French Basque, who were clear outliers on multiple measures of isolation. The finding of the Sorbs as only a minor genetic isolate demonstrates the need to genetically characterize putative population isolates, as they possess a wide range of levels of isolation because of their different demographic histories. PMID:21559053

  2. The legend of the Canadian horse: genetic diversity and breed origin.

    PubMed

    Khanshour, Anas; Juras, Rytis; Blackburn, Rick; Cothran, E Gus

    2015-01-01

    The Canadian breed of horse invokes a fascinating chapter of North American history and as such it is now a heritage breed and the national horse of Canada. The aims of this study were to determine the level of genetic diversity in the Canadian, investigate the possible foundation breeds and the role it had in the development of the US horse breeds, such as Morgan Horse. We tested a total of 981 horses by using 15 microsatellite markers. We found that Canadian horses have high values of genetic diversity indices and show no evidence of a serious loss of genetic diversity and the inbreeding coefficient was not significantly different from zero. Belgian, Percheron, Breton and Dales Pony, unlike the light French horses, may have common ancestries with the Canadian and could be important founders. However, the Shire and Clydesdale influenced the Canadian to a lesser extent than French and Belgian draft breeds. Furthermore, our finding indicated that there was no evidence of a clear relationship between Canadian and Oriental or Iberian breeds. Also, the Canadian likely contributed to the early development of the Morgan. Finally, these findings support the ancient legends of the Canadian Horse as North Americas first equine breed and the foundation bloodstock to many American breeds and may help in the management and breeding program of this outstanding breed in North America. PMID:25416795

  3. Genetic diversity of caprine Blastocystis from Peninsular Malaysia.

    PubMed

    Tan, Tian Chye; Tan, Peng Chiang; Sharma, Reuben; Sugnaseelan, Sumita; Suresh, Kumar Govind

    2013-01-01

    Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9%) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3%) followed by ST7 (41.1%), ST6 (41.1%), and ST3 (11.0%) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed. PMID:22961236

  4. Genetic diversity within Cryptosporidium parvum and related Cryptosporidium species.

    PubMed

    Xiao, L; Morgan, U M; Limor, J; Escalante, A; Arrowood, M; Shulaw, W; Thompson, R C; Fayer, R; Lal, A A

    1999-08-01

    To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidium isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genus Cryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characteristics, including C. wrairi, C. meleagridis, and C. felis, and the desert monitor isolate, clustered together or within C. parvum. Extensive genetic diversities were present among C. parvum isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate most Cryptosporidium spp. and C. parvum genotypes, but sequence analysis of the PCR product was needed to differentiate C. wrairi and C. meleagridis from some of the C. parvum genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal C. parvum isolates. PMID:10427023

  5. Ordering microbial diversity into ecologically and genetically cohesive units

    PubMed Central

    Shapiro, B. Jesse; Polz, Martin F.

    2014-01-01

    We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. Here, we discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a ‘reverse ecology’ approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity. PMID:24630527

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

    PubMed

    Aranguren-Mndez, J; Jordana, J; Gomez, M

    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 (H(E)) over all the populations varied between 0.637 and 0.684 in this study. The low G(ST) 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 D(A) distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

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

    PubMed Central

    Aranguren-Mndez, Jos; 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

  8. Whole mitochondrial genome genetic diversity in an Estonian population sample.

    PubMed

    Stoljarova, Monika; King, Jonathan L; Takahashi, Maiko; Aaspõllu, Anu; Budowle, Bruce

    2016-01-01

    Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25 % of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7 % in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85 %, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99 % for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions. PMID:26289416

  9. 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. PMID:26091176

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

    PubMed Central

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

  11. 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

  12. Genetic and clonal diversity of two cattail species, Typha latifolia and T. angustifolia (Typhaceae), from Ukraine.

    PubMed

    Tsyusko, Olga V; Smith, Michael H; Sharitz, Rebecca R; Glenn, Travis C

    2005-07-01

    Genetic and clonal diversity vary between two closely related cattail species (Typha angustifolia and T. latifolia) from Ukraine. This diversity was calculated from microsatellite data. Forty-eight percent of the total variation was partitioned between species, which formed distinct clusters in a dendrogram with no indication of hybrid populations. Typha angustifolia had higher heterozygosity at the species (H(es) = 0.66) and population (H(ep) = 0.49) levels than did T. latifolia (H(es) = 0.37 and H(ep) = 0.29, respectively). The higher number of alleles in T. angustifolia may be indicative of larger effective population sizes due to its higher seed production. Clonal diversity of T. angustifolia was lower than that of T. latifolia (N(g)/N(r) = 0.40 and 0.61, Simpson's D = 0.82 and 0.94, respectively). Correlations between clonal and genetic diversity were higher for T. latifolia than T. angustifolia, suggesting that the importance of factors and their interactions affecting this relationship are different for the two species. Latitudinal and longitudinal trends were not observed in either species despite the large sampling area. Population differentiation was relatively high with F(ST) of 0.24 and 0.29 for T. angustifolia and T. latifolia, respectively. Weak isolation by distance was observed for T. latifolia but not for T. angustifolia. PMID:21646138

  13. 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...

  14. Cryptic changes in the genetic structure of a highly clonal coral population and the relationship with ecological performance

    NASA Astrophysics Data System (ADS)

    Williams, Dana E.; Miller, M. W.; Baums, I. B.

    2014-09-01

    Elkhorn coral , Acropora palmata, relies heavily on clonal propagation and often displays low genotypic (clonal) diversity. Populations in the Florida Keys experienced rapid declines in tissue cover between 2004 and 2006, largely due to hurricanes and disease, but remained stable from 2006 to 2010. All elkhorn colonies in 150 m2 permanent study plots were genotyped in 2006 ( n = 15 plots) and 2010 ( n = 24 plots), and plots sampled in both years were examined for changes in allelic and genotypic diversity during this period of stable ecological abundance. Overall, genetic diversity of Florida plots was low and declined further over the 4-yr period; seven of the 36 original genets and two of 67 alleles (among five microsatellite loci) were lost completely from the sampled population, and an additional 15 alleles were lost from individual reefs. In 2010, Florida plots (~19 colonies) contained an average of 2.2 1.38 (mean SD) genets with a significant negative correlation between colony abundance and genotypic diversity. When scaled to total tissue abundance, genotypic diversity is even lower, with 43 % of genets below the size of sexual maturity. We examined the hypothesized positive relationship of local genotypic diversity with ecological performance measures. In Florida plots ( n = 15), genotypic diversity was not significantly correlated with tissue loss associated with chronic predation, nor with acute disease and storm-fragmentation events, though this relationship may be obscured by the low range of observed diversity and potential confounding with abundance. When more diverse plots in Curaao ( n = 9) were examined, genotypic diversity was not significantly correlated with resistance during an acute storm disturbance or rate of recovery following disturbance. Cryptic loss of genetic diversity occurred in the apparently stable Florida population and confirms that stable or even increasing abundance does not necessarily indicate genetic stability.

  15. 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. PMID:26606803

  16. 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. PMID:26881847

  17. Genetic diversity and population structure of Butea monosperma (Lam.) Taub.- a potential medicinal legume tree.

    PubMed

    Vashishtha, Amit; Jehan, Tabassum; Lakhanpaul, Suman

    2013-07-01

    Three molecular marker systems, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeats (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) were employed to investigate the genetic structure and diversity among the 14 natural populations of Butea monosperma collected from different geographical regions of India. Detected by 17 RAPD, 15 ISSR and 11 SRAP primer combinations, the proportions of polymorphic bands were 84.2 %, 77.2 % and 91.9 %, respectively, and the mean Nei's genetic distances among the populations were 0.13, 0.10 and 0.13, respectively. Partitioning of genetic variability by Analysis of molecular variance (AMOVA) revealed that the high genetic diversity was distributed within the populations. AMOVA also revealed that the coefficient of gene differentiation among populations based on FST was very high irrespective of markers used. The overall gene flow among populations (Nm) was very low. Cophenetic correlation coefficients of Nei's distance values and clustering pattern by Mental test were statistically significant for all three marker systems used but poor fit for ISSR data than for RAPD, SRAP and combined data set of all three markers. For all markers, a high similarity in dendrogram topologies was obtained, although some differences were observed with ISSR. The dendrogram obtained by RAPD, SRAP and combined data set of all three markers reflect relationship of most of the populations according to their geographic distribution. PMID:24431507

  18. Evaluation of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains.

    PubMed

    Liu, Jing-Yu; Ying, Zheng-He; Liu, Fang; Liu, Xin-Rui; Xie, Bao-Gui

    2012-04-01

    In this study, three molecular marker systems including sequence related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and inter-simple sequence repeats (ISSR) were screened to select polymorphisms of 24 main commercial strains of Lentinula edodes cultivated widely in China. Twenty-nine sequence characterized amplified region (SCAR) markers were developed to set up a dendrogram using UPMGA based on nucleotide sequences of some SRAP, RAPD, and ISSR polymorphic fragments. The grouping showed that the 24 strains were apparently clustered into five groups at a level of 0.68 similarity coefficient, and those that have similar breeding background clustered preferentially into the same subgroup. Results also revealed that the 24 strains had a low level of genetic diversity, and the breeding source of L. edodes should be broadened by exploiting wild types and introducing exotic strains. In addition, the tested strains of L. edodes could be clearly distinguished and identified from others by using different combinations of SCAR primers. Thus, results of this work demonstrated that SCAR was an excellent genetic marker system to characterize and investigate genetic diversity of L. edodes. Furthermore, this provided an alternative method to identify the genetic relationship of different strains of other fungi. PMID:22218569

  19. 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

  20. Genetic diversity and population history of the endangered killifish Aphanius baeticus.

    PubMed

    Gonzalez, Elena G; Pedraza-Lara, Carlos; Doadrio, Ignacio

    2014-01-01

    The secondary freshwater fish fauna of the western-Iberian Peninsula basin is primarily restricted to local coastal streams, and man-made salt evaporation ponds, etc., which are susceptible to periodical flood and drought events. Despite its uniqueness in ecological adaptation to high saltwater tolerance, very little is known about this fauna's population dynamics and evolutionary history. The killifish, Aphanius baeticus (Cyprinodontidae) is an endemic species restricted to river basins on Spain's southern Atlantic coastline, considered as "Endangered." In this study, the genetic structure, diversity and historical demography of A. baeticus were analyzed using mitochondrial (cytochrome b, N=131) and nuclear (4 out of 19 microsatellites tested, N=288) markers across its distribution range. The phylogenetic and networking reconstruction revealed subtle phylogeographic structuring. A scattered expansion at the beginning of the interglacial periods, coupled with posterior events of extinction and colonization caused by periodical cycles of flooding, could explain the absence of well-defined phylogenetic relationships among populations. Moreover, very low genetic diversity values and a weak population differentiation were detected. We proposed that dispersals allowed by periodic floods connecting river drainages may have promoted a wide genetic exchange among populations and could have contributed to the current genetic relatedness of these populations. PMID:24939890

  1. Genetic Differentiation and Relationships of Populations in the Cycas balansae Complex (Cycadaceae) and its Conservation Implications

    PubMed Central

    XIAO, LONG-QIAN; GONG, XUN

    2006-01-01

    Background and Aims The Cycas balansae complex is arguably a controversial group with regard to species delineation. Some taxonomists recognize a single polymorphic species while others distinguish five narrowly defined ones. The unresolved taxonomy has the potential to bring about significant problems for species conservation. Thus, an investigation to examine the genetic diversity and differentiation in the C. balansae complex was performed to determine the relationship of populations and to test whether the morphologically defined segregations represent genetically distinct units. Methods Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity in the C. balansae complex with a sample of 158 individuals from all extant populations in China. Key Results ISSR markers revealed low genetic diversity in all populations studied (HE and HO averaged 00639 and 00798 at the population level, respectively). Phenetic analysis showed that the C. balansae complex grouped into five clusters closely corresponding to the narrowly defined C. balansae, C. parvula, C. shiwandashanica, C. tanqingii and C. simplicipinna. Conclusions ISSR data suggest that the C. balansae complex has evolved into five genetically distinct units. These might be derived from a relatively widespread common ancestor through multiple vicariant events including geographical isolation resulting from the collision of the Indian plate with the Eurasian plate and from Pleistocene glaciations. In conservation, attention should be paid to each genetic unit. PMID:16517547

  2. Testing heterogeneity-diversity relationships in tropical forest restoration.

    PubMed

    Holl, Karen D; Stout, Victoria M; Reid, J Leighton; Zahawi, Rakan A

    2013-10-01

    Restoring small-scale habitat heterogeneity in highly diverse systems, like tropical forests, is a conservation challenge and offers an excellent opportunity to test factors affecting community assembly. We investigated whether (1) the applied nucleation restoration strategy (planting tree islands) resulted in higher habitat heterogeneity than more homogeneous forest restoration approaches, (2) increased heterogeneity resulted in more diverse tree recruitment, and (3) the mean or coefficient of variation of habitat variables best explained tree recruitment. We measured soil nutrients, overstory and understory vegetation structure, and tree recruitment at six sites with three 5- to 7-year-old restoration treatments: control (no planting), planted tree islands, and conventional, mixed-species tree plantations. Canopy openness and soil base saturation were more variable in island treatments than in controls and plantations, whereas most soil nutrients had similar coefficients of variation across treatments, and bare ground was more variable in control plots. Seedling and sapling species density were equivalent in plantations and islands, and were substantially higher than in controls. Species spatial turnover, diversity, and richness were similar in island and plantation treatments. Mean canopy openness, rather than heterogeneity, explained the largest proportion of variance in species density. Our results show that, whereas canopy openness and soil base saturation are more heterogeneous with the applied nucleation restoration strategy, this pattern does not translate into greater tree diversity. The lack of a heterogeneity-diversity relationship is likely due to the fact that recruits respond more strongly to mean resource gradients than variability at this early stage in succession, and that seed dispersal limitation likely reduces the available species pool. Results show that planting tree islands facilitates tree recruitment to a similar degree as intensive plantation-style restoration strategies. PMID:23525802

  3. Genetic structure and genetic diversity of single-variety Lonicera macranthoides populations in China, as indicated by SCoT markers.

    PubMed

    Chen, D X; Li, L Y; Zhang, X; Wang, Y

    2015-01-01

    Lonicera macranthoides is an important traditional Chinese herb. The lack of information regarding the genetic structure and genetic relationships among its cultivars has hindered the conservation and utilization of this resource. This study used start codon targeted markers to assess the genetic diversity and other genetic characteristics of five single-variety L. macranthoides populations in China. Using 22 primers produced a total of 266 bands, of which 227 were polymorphic, indicating a high level of polymorphism. At the species level, genetic diversity was high: percentage of polymorphic loci (PPB) = 85.34%, effective number of alleles (NE) = 1.3479, Nei's gene diversity (H) = 0.2075, and Shannon's information index (Hsp, species level) = 0.3198. However, at the varietal population level, genetic diversity was lower, with averages of: PPB = 19.74%, NE = 1.0946, H = 0.0561, Hpop = 0.0850 (population level). Nei's genetic differentiation coefficient was 0.7319, which is consistent with Shannon's population genetic differentiation coefficient (0.7324). This indicates that most of the genetic variation in this species exists among the varietal populations. The differentiation among varieties may have been caused by artificial selection, mode of reproduction, and barriers to gene flow (0.1831). The genetic similarity coefficient ranged from 0.7222 to 0.9419. Phylogenetic analysis showed the five varieties to form two major clades. Results suggest that cultivar breeders should strengthen the exchange of germplasm and increase the mutual penetration of useful genes, which would broaden the hereditary basis of L. macranthoides. PMID:26214488

  4. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    PubMed

    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

  5. 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. PMID:25859251

  6. Evaluation of the genetic diversity of avian paramyxovirus type 4

    PubMed Central

    Nayak, Baibaswata; Nayak, Shreeraj; Paldurai, Anandan; Kumar, Sachin; De Nardi, Roberta; Terregino, Calogero; Collins, Peter L; Samal, Siba K

    2012-01-01

    Avian paramyxoviruses (APMVs) belong to the genus Avulavirus in the family Paramyxoviridae and include at least nine serotypes, APMV-1 to -9, as well as two additional provisional serotypes. Newcastle disease virus (NDV), which comprises APMV-1, is the most extensively studied APMV because it is an important poultry pathogen. A moderate level of antigenic and genetic diversity is recognized for APMV-1 isolates, but our knowledge of the antigenic and genetic diversity of the other APMV serotypes is limited. APMV-4 is frequently isolated from waterfowl around the world. To date complete genome sequences of APMV-4 are available for only strains, which were isolated from ducks in Hong Kong, Korea and Belgium over a period of 37 years. We have carried out genome sequencing from the nucleocapsid (N) gene-end signal to the polymerase (L) gene-start signal of five APMV-4 strains recently isolated from Italy. Each of the eight APMV-4 strains has the same F protein cleavage site, DIQPR?F. They also share a high level of nucleotide and amino acid sequence identity: for example, the F and HN glycoproteins have greater than 97% sequence identity between the various strains. Thus, comparison of these eight strains of APMV-4 did not provide evidence of substantial diversity, in contrast to similar studies with APMV-2, -3, and -6, in which the F and HN glycoproteins exhibited up to 20-30% amino acid sequence variation within a subgroup. Reciprocal cross-HI assay using post infection chicken sera also failed to detect significant antigenic variation among the available APMV-4 strains. PMID:23178589

  7. 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

  8. 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

  9. 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 or an environmental change. PMID:26207812

  10. Role of telomere dysfunction in genetic intratumor diversity.

    PubMed

    Genescà, Anna; Pampalona, Judit; Frías, Cristina; Domínguez, Daniel; Tusell, Laura

    2011-01-01

    Most solid tumors are unable to maintain the stability of their genomes at the chromosome level. Indeed, cancer cells display highly rearranged karyotypes containing translocations, amplifications, deletions, and gains and losses of whole chromosomes, which reshuffle steadily. This chromosomal instability most likely occurs early in the development of cancer, and may represent an important step in promoting the multiple genetic changes required for the initiation and/or progression of the disease. Different mechanisms may underlie chromosome instability in cancer cells, but a prominent role for telomeres, the tip of linear chromosomes, has been determined. Telomeres are ribonucleoprotein structures that prevent natural chromosome ends being recognized as DNA double-strand breaks, by adopting a loop structure. Loss of telomere function appears from either alteration on telomere-binding proteins or from the progressive telomere shortening that normally occurs under physiological conditions in the majority of cells in tissues. Importantly, unmasked telomeres may either trigger the senescent phenotype that has been linked to the aging process or may initiate the chromosome instability needed for cancer development, depending on the integrity of the DNA damage checkpoint responses. Telomere dysfunction contributes to chromosome instability through end-to-end chromosome fusions entering breakage-fusion-bridge (BFB) cycles. Resolution of chromatin bridge intermediates is likely to contribute greatly to the generation of segmental chromosome amplification events, unbalanced chromosome rearrangements, and whole chromosome aneuploidy. Noteworthy is the fact that telomere length heterogeneity among individuals may directly influence the scrambling of the genome at tumor initiation. However, reiterated BFB cycles would randomly reorganize the cell karyotype, thus increasing the genetic diversity that characterizes tumor cells. Even though a direct link is still lacking, multiple evidence lead one to believe that telomere dysfunction directly contributes to cancer development in humans. The expansion of highly unstable cells due to telomere dysfunction enhances the genetic diversity needed to fuel specific mutations that may promote cell immortalization and the acquisition of a tumor phenotype. PMID:21925300

  11. Late Quaternary loss of genetic diversity in muskox (Ovibos)

    PubMed Central

    MacPhee, Ross DE; Tikhonov, Alexei N; Mol, Dick; Greenwood, Alex D

    2005-01-01

    Background The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen. Results Two classes of haplotypes were detected in the fossil material. "Surviving haplotypes" (SHs), closely similar or identical to haplotypes found in modern muskoxen and ranging in age from ~22,000 to ~160 yrbp, were found in all New World samples as well as some samples from northeastern Asia. "Extinct haplotypes" (EHs), dating between ~44,000 and ~18,000 yrbp, were found only in material from the Taimyr Peninsula and New Siberian Islands in northeastern Asia. EHs were not found in the Holocene muskoxen specimens available for this study, nor have they been found in other studies of extant muskox populations. Conclusion We provisionally interpret this evidence as showing that genetic variability was reduced in muskoxen after the Last Glacial Maximum but before the mid-Holocene, or roughly within the interval 18,000-4,000 yrbp. Narrowing this gap further will require the recovery of more fossils and additional genetic information from this interval. PMID:16209705

  12. 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 or an environmental change. PMID:26207812

  13. Genetic relationships among breeds of beef cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to estimate genetic distance among 16 populations of beef cattle from within the U.S. Thirty-three microsatellite markers representing 26 autosomes were used. MicroSatellite Analyzer 3.15 (MSA) program was used to quantify number of alleles per marker, and observed and expected het...

  14. Genetic diversity of Ostreopsis ovata (Dinophyceae) from Malaysia.

    PubMed

    Pin, L C; Teen, L P; Ahmad, A; Usup, G

    2001-05-01

    The genus Ostreopsis is an important component of benthic and epiphytic dinoflagellate assemblages in coral reefs and seaweed beds of Malaysia. Members of the species may produce toxins that contribute to ciguatera fish poisoning. In this study, two species have been isolated and cultured, Ostreopsis ovata and Ostreopsis lenticularis. Analyses of the 5.8S subunit and internal transcribed spacer regions ITS1 and ITS2 of the ribosomal RNA gene sequences of these two species showed that they are separate species, consistent with morphological designations. The nucleotide sequences of the 5.8S subunit and ITS1 and ITS2 regions of the rRNA gene were also used to evaluate the interpopulation and intrapopulation genetic diversity of O. ovata found in Malaysian waters. Results showed a low level of sequence divergence within populations. At the interpopulation level, the rRNA gene sequence distinguished two groups of genetically distinct strains, representative of a Malacca Straits group (isolates from Port Dickson) and a South China Sea group (isolates from Pulau Redang and Kota Kinabalu). Part of the sequences in the ITS regions may be useful in the design of oligonucleotide probes specific for each group. Results from this study show that the ITS regions can be used as genetic markers for taxonomic, biogeographic, and fine-scale population studies of this species. PMID:14961362

  15. Molecular and genetic diversity in the metastatic process of melanoma.

    PubMed

    Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran

    2014-05-01

    Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. PMID:24399611

  16. Genetic Variation and Phylogenetic Relationships of Indian Buffaloes of Uttar Pradesh

    PubMed Central

    Joshi, Jyoti; Salar, R. K.; Banerjee, Priyanka; S, Upasna; Tantia, M. S.; Vijh, R. K.

    2013-01-01

    India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes. PMID:25049904

  17. High-Resolution Analysis of Intrahost Genetic Diversity in Dengue Virus Serotype 1 Infection Identifies Mixed Infections

    PubMed Central

    Henn, Matthew R.; Zody, Michael C.; Tricou, Vianney; Nguyet, Nguyen Minh; Charlebois, Patrick; Lennon, Niall J.; Green, Lisa; de Vries, Peter J.; Hien, Tran Tinh; Farrar, Jeremy; van Doorn, H. Rogier; de Jong, Menno D.; Birren, Bruce W.; Holmes, Edward C.; Simmons, Cameron P.

    2012-01-01

    Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia. PMID:22090119

  18. Habitat Loss other than Fragmentation per se Decreased Nuclear and Chloroplast Genetic Diversity in a Monoecious Tree

    PubMed Central

    Shen, Dong-Wei; Chen, Xiao-Yong

    2012-01-01

    Generally, effect of fragmentation per se on biodiversity has not been separated from the effect of habitat loss. In this paper, using nDNA and cpDNA SSRs, we studied genetic diversity of Castanopsis sclerophylla (Lindl. & Paxton) Schotty populations and decoupled the effects of habitat loss and fragmentation per se. We selected seven nuclear and six cpDNA microsatellite loci and genotyped 460 individuals from mainland and island populations, which were located in the impoundment created in 1959. Number of alleles per locus of populations in larger habitats was significantly higher than that in smaller habitats. There was a significant relationship between the number of alleles per locus and habitat size. Based on this relationship, the predicted genetic diversity of an imaginary population of size equaling the total area of the islands was lower than that of the global population on the islands. Re-sampling demonstrated that low genetic diversity of populations in small habitats was caused by unevenness in sample size. Fisher's ? index was similar among habitat types. These results indicate that the decreased nuclear and chloroplast genetic diversity of populations in smaller habitats was mainly caused by habitat loss. For nuclear and chloroplast microsatellite loci, values of FST were 0.066 and 0.893, respectively, and the calculated pollen/seed dispersal ratio was 162.2. When separated into pre-and post-fragmentation cohorts, pollen/seed ratios were 121.2 and 189.5, respectively. Our results suggest that habitat loss explains the early decrease in genetic diversity, while fragmentation per se may play a major role in inbreeding and differentiation among fragmented populations and later loss of genetic diversity. PMID:22723951

  19. [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 microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species. PMID:15640074

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

    PubMed

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

    2015-06-01

    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. PMID:25892717

  1. Mammalian phylogenetic diversity-area relationships at a continental scale.

    PubMed

    Mazel, Florent; Renaud, Julien; Guilhaumon, Franois; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

    2015-10-01

    In analogy to the species-area relationship (SAR), one of the few laws in ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR), since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e., standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and nonrandom spatial distribution of evolutionary history on the PDAR. We find that, for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

  2. Mammalian phylogenetic diversity-area relationships at a continental scale

    PubMed Central

    Mazel, Florent; Renaud, Julien; Guilhaumon, François; Mouillot, David; Gravel, Dominique; Thuiller, Wilfried

    2015-01-01

    In analogy to the species-area relationship (SAR), one of the few laws in Ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR) since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e. standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and non random spatial distribution of evolutionary history on the PDAR. We find that for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD. PMID:26649401

  3. Genetic diversity and population structure in Brazilian Mangalarga Marchador horses.

    PubMed

    DeAssis, J B; DeLaat, D M; Peixoto, M G C D; Bergmann, J A G; Fonseca, C G; Carvalho, M R S

    2009-01-01

    One hundred and fifteen unrelated Mangalarga Marchador horses were sampled from three geographically distinct regions of Minas Gerais State, Brazil (South, Southeast, and Northeast) and tested for 10 microsatellite loci. Genetic diversity and population structure parameters were estimated with ARLEQUIN 3.0, CERVUS 2.0, POPGENE 1.31, GENEPOP on the web, STRUCTURE 2.0, and SPAGEDI 1.2 software packages. Under Hardy-Weinberg assumptions, seven markers were at equilibrium (LEX014, LEX017, LEX019, SGCV23, TKY321, VHL20, and VIASH39), while two (ASB3 and LEX031) presented significant homozygote excess. Seventy-four alleles were identified in these nine markers, with a mean of 8.22 alleles. Mean heterozygosity was 0.637 and polymorphism information content was 0.662. Markers ASB3, LEX019, SGCV23, TKY321, and VHL20 were highly informative (PIC >0.7) and may be useful for eventual expansion of parentage test panels. The F(ST) value (0.0562) indicated relatively little geographical structure. However, based on a Bayesian-based cluster analysis under a three-cluster model, 94% of the 115 individuals were correctly assigned to the subpopulations from where they were sampled. Mean pairwise f was relatively high (0.11), and in spite of the efforts towards non-consanguineous sampling, 1% of the pairs of individuals shared over 50% of the alleles. These results strongly suggest that the population is genetically structured. Under a conservation genetics approach, two strategies are recommended: avoidance of crosses between highly endogamic individuals and stimulation of crosses between individuals from those regions for which low genetic flow was identified. PMID:20082264

  4. Genetic breeding and diversity of the genus Passiflora: progress and perspectives in molecular and genetic studies.

    PubMed

    Cerqueira-Silva, Carlos Bernard M; Jesus, Onildo N; Santos, Elisa S L; Corra, Ronan X; Souza, Anete P

    2014-01-01

    Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit. PMID:25196515

  5. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies

    PubMed Central

    Cerqueira-Silva, Carlos Bernard M.; Jesus, Onildo N.; Santos, Elisa S. L.; Corrêa, Ronan X.; Souza, Anete P.

    2014-01-01

    Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit. PMID:25196515

  6. SSR Marker Analysis of Genetic Relationships within Hydrangea paniculata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 taxa of Hydrangea paniculata Sieb. The SSR loci were highly variable among the taxa, producing a mean of 5.8 alleles per locus. Three cultivars (Boskoop, Compact Grandiflora and Webb) were either identic...

  7. SSR Marker Analysis of Genetic Relationships within Hydrangea Macrophylla

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity studies using 39 SSR markers were carried out with 114 taxa of H. macrophylla. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. Subspecies serrata contained nearly t...

  8. High Spatial Genetic Structure and Genetic Diversity in Chinese Populations of Sitobion miscanthi (Hemiptera: Aphididae).

    PubMed

    Wang, Yongmo; Hereward, James P; Zhang, Guoan

    2016-02-01

    The wheat aphid, Sitobion miscanthi Takahashi, a serious wheat pest, was previously considered to be highly migratory and anholocyclic in China. We recorded 69 alleles and 346 multilocus genotypes among 708 aphid individuals from 12 populations in China using 5 microsatellite loci. This genotypic diversity indicates that at least some holocyclic lineages exist. Bayesian clustering analysis revealed that there are two differentiated genetic groups of S. misanthi, one northern and one southern, in China. Principal coordinates analysis of population genetic distance, pairwise F(ST)'s, and network analysis of individual minimum spanning distance also supported the division. Low levels of migration were detected between the northern and southern sampling sites, but the high genetic differentiation does not support the hypothesis S. miscanthi overwinters in the south and migrates to the north in the spring annually. PMID:26487744

  9. Update on the Comparative Assessment of Genetic Diversity Between Accessible and Remote Potato Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is limited information on the organization of potato genetic diversity (GD) in natural habitats. Answering questions on that topic has significant implications for germplasm conservation -- for example, targeting habitats and populations with greater genetic richness or distinctiveness for col...

  10. 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...

  11. tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns.

    PubMed

    Baraket, G; Abdelkrim, A B; Salhi-Hannachi, A

    2015-01-01

    Cytoplasmic chloroplast DNA was explored to establish genetic relationships among Ficus carica cultivars and elucidate the molecular evolution of the species. The results suggest the occurrence of haplotype and nucleotide diversity. Conserved group I intron sequence motifs were detected and showed a common secondary structure, despite the presence of some mutations on their sequences. The neighbor-joining dendrogram showed a continuous diversity that characterizes local resources. The maximum parsimony tree, with an RI index of 0.507, indicated minimal homoplasy within the data set. Furthermore, our results demonstrate that the trnL intron is the seat of numerous substitutions. Herein, new insight on the mechanism involved in the evolution of the trnL intron in the fig is presented. From the study, it appears that there is an explicit rejection of the null hypothesis in F. carica. A scenario of positive selection and recent expansion of F. carica genotypes across Tunisia seems to be retained. PMID:25966152

  12. AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping

    PubMed Central

    Campbell, Michael C.; Tishkoff, Sarah A.

    2010-01-01

    Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. PMID:18593304

  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, B?etislav; Modr, 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 in cyanobacterial symbionts of thalloid bryophytes.

    PubMed

    Rikkinen, Jouko; Virtanen, Viivi

    2008-01-01

    Two species of thalloid liverworts, Blasia pusilla and Cavicularia densa, form stable symbioses with nitrogen-fixing cyanobacteria. Both bryophytes promote the persistence of their cyanobacterial associations by producing specialized gemmae, which facilitate the simultaneous dispersal of the host and its nitrogen-fixing symbionts. Here the genetic diversity of cyanobacterial symbionts of Blasia and Cavicularia is examined. The results indicate that the primary symbionts of both bryophytes are closely related and belong to a specific group of symbiotic Nostoc strains. Related strains have previously been reported from hornworts and cycads, and from many terricolous cyanolichens. The evolutionary origins of all these symbioses may trace back to pre-Permian times. While the laboratory strain Nostoc punctiforme PCC 73102 has been widely used in experimental studies of bryophyte-Nostoc associations, sequence-identical cyanobionts have not yet been identified from thalloid liverworts in the field. PMID:18325923

  15. [Genetic diversity of Besermyan based on mitochondrial DNA polymorphism].

    PubMed

    Grosheva, A N; Shneider, Yu V; Morozova, I Yu; Zhukova, O V; Rychkov, S Yu

    2013-11-01

    The first data on mtDNA diversity in Besermyan, the Finno-Ugric ethnic group, related to Udmurts, are presented. An analysis of mtDNA polymorphism showed that Besermyan stood out from the other populations of Volga-Ural region due to the presence of a large proportion of the mongoloid component. The sample of Besermyan contained East Eurasian haplotypes not detected in ethnic populations of the Volga region and Cisurals, while they were detected in South Siberia, mostly among Turkic-speaking populations. An analysis of the genetic distances between Besermyan and the neighboring ethnic groups showed that Besermyan were distant from other populations of Volga-Ural region and close to Turkic-speaking populations of South Siberia. Thus, the data obtained favor the suggestion on the mixed Udmurto-Turkic origin of Besermyan. PMID:25470935

  16. Genetic structure and phylogenetic relationships of the Polish Heavy horse.

    PubMed

    Iwa?czyk, Ewa; Juras, Rytis; Cholewi?ski, Grzegorz; Cothran, E Gus

    2006-01-01

    In this study a wide range of genetic markers (12 microsatellites, 7 blood-group loci, 10 blood-protein loci) and mitochondrial DNA (mtDNA) were used to assess genetic diversity in Polish Heavy horses. Three random samples were sequenced for 421 bp of the mitochondrial D-loop region, but no clear phylogenetic patterns were seen in mtDNA variation. Both heterozygosity and diversity levels are fairly high in Polish Heavy horses. In phylogenetic analysis the draught horses form a distinct cluster that pairs with the true pony breeds. Within this 'cold-blooded' group, the Polish Heavy Horse clusters most closely with the Posavina breed from Croatia and the Breton breed from France. From the standpoint of genetic conservation, the Polish Heavy Horse does not appear to be in jeopardy. PMID:17132900

  17. Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae: Culex spp.) from the Sonoran Desert of North America

    PubMed Central

    Pfeiler, Edward; Flores-Lpez, Carlos A.; Mada-Vlez, Jess Gerardo; Escalante-Verdugo, Juan; Markow, Therese A.

    2013-01-01

    The population genetics and phylogenetic relationships of Culex mosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding to Cx. quinquefasciatus, Cx. tarsalis, and two unidentified species, Culex sp. 1 and sp. 2. Culex quinquefasciatus was found at all localities and was the most abundant species collected. Culex tarsalis was collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species of Culex were most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower in Cx. quinquefasciatus compared with the other three species. Analysis of molecular variance revealed little structure among seven populations of Cx. quinquefasciatus, whereas significant structure was found between the two populations of Cx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found for Cx. tarsalis. Possible explanations for the large differences in genetic diversity between Cx. quinquefasciatus and the other species of Culex are presented. PMID:24302868

  18. Musa genetic diversity revealed by SRAP and AFLP.

    PubMed

    Youssef, Muhammad; James, Andrew C; Rivera-Madrid, Renata; Ortiz, Rodomiro; Escobedo-GraciaMedrano, Rosa María

    2011-03-01

    The sequence-related amplified polymorphism (SRAP) technique, aimed for the amplification of open reading frames (ORFs), vis-â-vis that of the amplified fragment length polymorphisms (AFLP) were used to analyze the genetic variation and relationships among forty Musa accessions; which include commercial cultivars and wild species of interest for the genetic enhancement of Musa. A total of 403 SRAP and 837 AFLP amplicons were generated by 10 SRAP and 15 AFLP primer combinations, of which 353 and 787 bands were polymorphic, respectively. Both cluster analysis of unweighted pair-grouping method with arithmetic averages (UPGMA) and principal coordinate (PCO) analysis separated the forty accessions into their recognized sections (Eumusa, Australimusa, Callimusa and Rhodochlamys) and species. The percentage of polymorphism amongst sections and species and the relationships within Eumusa species and subspecies varied between the two marker systems. In addition to its practical simplicity, SRAP exhibited approximately threefold more specific and unique bands than AFLP, 37 and 13%, respectively. SRAP markers are demonstrated here to be proficient tools for discriminating amongst M. acuminata, M. balbisiana and M. schizocarpa in the Eumusa section, as well as between plantains and cooking bananas within triploid cultivars. PMID:20803102

  19. 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

  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. Genetic diversity of Echinococcus granulosus in center of Iran.

    PubMed

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

    2014-08-01

    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

  2. Clan, Language, and Migration History Has Shaped Genetic Diversity in Haida and Tlingit Populations From Southeast Alaska

    PubMed Central

    Schurr, Theodore G.; Dulik, Matthew C.; Owings, Amanda C.; Zhadanov, Sergey I.; Gaieski, Jill B.; Vilar, Miguel G.; Ramos, Judy; Moss, Mary Beth; Natkong, Francis

    2013-01-01

    The linguistically distinctive Haida and Tlingit tribes of Southeast Alaska are known for their rich material culture, complex social organization, and elaborate ritual practices. However, much less is known about these tribes from a population genetic perspective. For this reason, we analyzed mtDNA and Y-chromosome variation in Haida and Tlingit populations to elucidate several key issues pertaining to the history of this region. These included the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family, specifically, the inclusion of Haida with Athapaskan, Eyak, and Tlingit in the language family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. Our analysis indicates that, while sharing a “northern” genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region. PMID:22549307

  3. 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...

  4. Delineating genetic relationships among the Maya.

    PubMed

    Ibarra-Rivera, Lisa; Mirabal, Sheyla; Regueiro, Manuela M; Herrera, Rene J

    2008-03-01

    By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire. PMID:18000891

  5. Comparison of statistical methods for assessment of population genetic diversity by DNA fingerprinting

    SciTech Connect

    Leonard, T.; Roth, A.; Gordon, D.; Wessendarp, T.; Smith, M.K.; Silbiger, R.; Torsella, J.

    1995-12-31

    The advent of newer techniques for genomic characterization, e.g., Random Amplified Polymorphic DNA (RAPD) fingerprinting, has motivated development of a number of statistical approaches for creating hypothesis tests using this genetic information. The authors specific interest is methods for deriving relative genetic diversity measures of feral populations subjected to varying degrees of environmental impacts. Decreased polymorphism and loss of alleles have been documented in stressed populations of some species as assayed by allozyme analysis and, more recently, by DNA fingerprinting. Multilocus fingerprinting techniques (such as RAPDS) differ from allozyme analysis in that they do not explicitly yield information of allelism and heterozygosity. Therefore, in order to infer these parameters, assumptions must be made concerning the relationship of observed data to the underlying DNA architecture. In particular, assessments of population genetic diversity from DNA fingerprint data have employed at least three approaches based on different assumptions about the data. The authors compare different statistics, using a previously presented set of RAPD fingerprints of three populations of brown bullhead catfish. Furthermore, the behavior of these statistics is examined--as the sample sizes of fish/population and polymorphisms/fish are varied. Sample sizes are reduced either randomly or, in the case of polymorphisms (which are electrophoretic bands), systematically pruned using the criteria of high reproducibility between duplicate samples for inclusion of data. Implications for sampling individuals and loci in assessments of population genetic diversities are discussed. Concern about population N value and statistical power is very relevant to field situations where individuals available for sampling may be limited in number.

  6. Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide

    PubMed Central

    Lam, Joseph S.; Taylor, Véronique L.; Islam, Salim T.; Hao, Youai; Kocíncová, Dana

    2011-01-01

    Lipopolysccharide (LPS) is an integral component of the Pseudomonas aeruginosa cell envelope, occupying the outer leaflet of the outer membrane in this Gram-negative opportunistic pathogen. It is important for bacterium–host interactions and has been shown to be a major virulence factor for this organism. Structurally, P. aeruginosa LPS is composed of three domains, namely, lipid A, core oligosaccharide, and the distal O antigen (O-Ag). Most P. aeruginosa strains produce two distinct forms of O-Ag, one a homopolymer of D-rhamnose that is a common polysaccharide antigen (CPA, formerly termed A band), and the other a heteropolymer of three to five distinct (and often unique dideoxy) sugars in its repeat units, known as O-specific antigen (OSA, formerly termed B band). Compositional differences in the O units among the OSA from different strains form the basis of the International Antigenic Typing Scheme for classification via serotyping of different strains of P. aeruginosa. The focus of this review is to provide state-of-the-art knowledge on the genetic and resultant functional diversity of LPS produced by P. aeruginosa. The underlying factors contributing to this diversity will be thoroughly discussed and presented in the context of its contributions to host–pathogen interactions and the control/prevention of infection. PMID:21687428

  7. Genetic diversity of Toxoplasma gondii in animals and humans

    PubMed Central

    Sibley, L. David; Khan, Asis; Ajioka, James W.; Rosenthal, Benjamin M.

    2009-01-01

    Toxoplasma gondii is one of the most widespread parasites of domestic, wild, and companion animals, and it also commonly infects humans. Toxoplasma gondii has a complex life cycle. Sexual development occurs only in the cat gut, while asexual replication occurs in many vertebrate hosts. These features combine to create an unusual population structure. The vast majority of strains in North America and Europe fall into three recently derived, clonal lineages known as types I, II and III. Recent studies have revealed that South American strains are more genetically diverse and comprise distinct genotypes. These differences have been shaped by infrequent sexual recombination, population sweeps and biogeography. The majority of human infections that have been studied in North America and Europe are caused by type II strains, which are also common in agricultural animals from these regions. In contrast, several diverse genotypes of T. gondii are associated with severe infections in humans in South America. Defining the population structure of T. gondii from new regions has important implications for transmission, immunogenicity and pathogenesis. PMID:19687043

  8. 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. PMID:22537413

  9. The genetic diversity of the Vigna angularis complex in Asia.

    PubMed

    Zong, Xu Xiao; Kaga, Akito; Tomooka, Norihiko; Wang, Xin Wang; Han, Ouk Kyu; Vaughan, Duncan

    2003-08-01

    A selected set of accessions of components of the azuki bean (Vigna angularis) complex comprising 123 cultivated accessions and 23 wild or weedy accessions from Bhutan, China (including Taiwan), India, Japan, Korea, and Nepal was analyzed using amplified fragment length polymorphism (AFLP) methodology. Using 12 AFLP primer pairs, 580 unambiguous bands were generated, 313 (53.9%) of which were polymorphic among azuki bean accessions. All 580 bands were used to assess phenotypic (band) and genetic (nucleotide) diversity among the 146 azuki bean accessions. The results indicate five major groups of azuki bean germplasm primarily associated with geographic origin of accessions and their status: wild, weedy, or cultivated. These five groups are (i) Himalayan wild, (ii) Nepal-Bhutan cultivated, (iii) Chinese wild, (iv) Taiwan wild - Bhutan cultivated, and (v) northeast Asian accessions. Within the northeast Asian accessions, three subgroups are present. These consist of (v1) Japanese complex - Korean cultivated, (v2) Japanese cultivated, and (v3) Chinese cultivated accessions. The results suggest domestication of azuki bean occurred at least twice, once in the Himalayan region of southern Asia and once in northeast Asia. The remarkable diversity of azuki bean germplasm in the Himalayan region compared with other regions suggests this is a rich source of germplasm for plant breeding. The results suggest there are important gaps in the germplasm collections of azuki bean and its close relatives from various parts of Asia and that specific collecting missions for Vigna germplasm related to azuki bean in the highlands of subtropical Asia are needed. PMID:12897872

  10. Structural diversity in Salmonella O antigens and its genetic basis.

    PubMed

    Liu, Bin; Knirel, Yuriy A; Feng, Lu; Perepelov, Andrei V; Senchenkova, Sof'ya N; Reeves, Peter R; Wang, Lei

    2014-01-01

    This review covers the structures and genetics of the 46 O antigens of Salmonella, a major pathogen of humans and domestic animals. The variation in structures underpins the serological specificity of the 46 recognized serogroups. The O antigen is important for the full function and virulence of many bacteria, and the considerable diversity of O antigens can confer selective advantage. Salmonella O antigens can be divided into two major groups: those which have N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) and those which have galactose (Gal) as the first sugar in the O unit. In recent years, we have determined 21 chemical structures and sequenced 28 gene clusters for GlcNAc-/GalNAc-initiated O antigens, thus completing the structure and DNA sequence data for the 46 Salmonella O antigens. The structures and gene clusters of the GlcNAc-/GalNAc-initiated O antigens were found to be highly diverse, and 24 of them were found to be identical or closely related to Escherichia coli O antigens. Sequence comparisons indicate that all or most of the shared gene clusters were probably present in the common ancestor, although alternative explanations are also possible. In contrast, the better-known eight Gal-initiated O antigens are closely related both in structures and gene cluster sequences. PMID:23848592

  11. Genetic diversity of ITS sequences of Bursaphelenchus xylophilus.

    PubMed

    Cardoso, J M S; Fonseca, L; Abrantes, I

    2012-01-01

    The sequence variation of internal transcribed spacer (ITS) regions of ribosomal DNA has been routinely used for species identification and species-level phylogeny of the pinewood nematode, Bursaphelenchus xylophilus. In this study, the intraspecies ITS genetic diversity of B. xylophilus was evaluated. Three pinewood nematode isolates from the United States, Japan, and Portugal were used for polymerase chain reaction (PCR) ITS region amplification and sequencing. Multiple peaks were observed in sequencing chromatograms from ITS regions of American and Japanese isolates, suggesting the presence of more than one ribosomal sequence for each isolate. PCR products were further cloned and 10 clones of each isolate were subsequently sequenced. Additionally, the ITS regions of individual nematodes from each isolate were amplified, cloned and sequenced. Among the 3 B. xylophilus isolates analyzed, an intraspecific and intra-isolate molecular variability was found. The intra-isolate ITS molecular diversity in the American isolate was higher than that in the Japanese and Portuguese isolates. However, the level of sequence variation observed within isolates was about the same as that described among ITS repeats within individuals. PMID:23096915

  12. Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity

    PubMed Central

    Mazel, Florent; Guilhaumon, François; Mouquet, Nicolas; Devictor, Vincent; Gravel, Dominique; Renaud, Julien; Cianciaruso, Marcus Vinicius; Loyola, Rafael Dias; Diniz-Filho, José Alexandre Felizola; Mouillot, David; Thuiller, Wilfried

    2014-01-01

    Aim To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them to ‘classical’ hotspots based on species richness (SR) only. Location Global Methods SR, PD & FD were computed for 782 terrestrial ecoregions using distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework that incorporates the species relative coverage in each ecoregion. We build large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each diversity facet. Finally we defined hotspots as the top-ranked ecoregions. Results While ignoring species relative coverage led to a relative good congruence between biome top ranked SR, PD and FD hotspots, ecoregions harboring a rich and abundantly represented evolutionary history and functional diversity did not match with top ranked ecoregions defined by species richness. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than species richness as a function of area. Main conclusions The fact that PD/FD reach faster their maximal value than SR may suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it is quantified at global scale and should have important consequences in conservation. Incorporating species relative coverage into the delineation of multifaceted hotspots of diversity lead to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail at preserving those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at global scale. PMID:25071413

  13. Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations.

    PubMed

    Magalhes, Vanessa; Abrantes, Joana; Munz-Pajares, Antonio Jess; 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. PMID:26307416

  14. Antimicrobial resistance and genetic diversity of Escherichia coli isolated from humans and foods

    PubMed Central

    Melo, Daniela Benevides; Menezes, Ana Paula de Oliveira; Reis, Joice Neves; Guimarães, Alaíse Gil

    2015-01-01

    Antibiotic resistance has increased in recent years, raising the concern of public health authorities. We conducted a study of Escherichia coli isolates obtained from human and food samples to assess the prevalence of antimicrobial resistance and to determine the genotype and clonal relationship of 84 E. coli isolates (48 from humans and 36 from foods). An antimicrobial susceptibility test was performed using the disk diffusion method. Virulence factors were evaluated by multiplex PCR, and the clonal relationship among the resistant isolates was studied by Pulsed Field Gel Electrophoresis (PFGE). All isolates were susceptible to ceftriaxone. Overall, 26%, 20.2%, 15.4% and 6% of the isolates were resistant to tetracycline, ampicillin, sulfamethoxazole/trimethoprim and cephalotin, respectively. Twenty two percent of the isolates exhibited resistance to more than one antimicrobial agent. Multiple-drug resistance was mostly observed in the human isolates and involved the antibiotics ampicillin and tetracycline. None of the six virulence genes were identified among the isolates. Analysis of genetic diversity by PFGE of 31 resistant isolates, revealed 29 distinct restriction patterns. In conclusion, E. coli from humans and foods are resistant to commonly used antibiotics and are highly genetically diverse. In this setting, inappropriate use of antibiotics may be a cause of high resistance rate instead of clonal spread. PMID:26691477

  15. Antimicrobial resistance and genetic diversity of Escherichia coli isolated from humans and foods.

    PubMed

    Melo, Daniela Benevides; Menezes, Ana Paula de Oliveira; Reis, Joice Neves; Guimarães, Alaíse Gil

    2015-12-01

    Antibiotic resistance has increased in recent years, raising the concern of public health authorities. We conducted a study of Escherichia coli isolates obtained from human and food samples to assess the prevalence of antimicrobial resistance and to determine the genotype and clonal relationship of 84 E. coli isolates (48 from humans and 36 from foods). An antimicrobial susceptibility test was performed using the disk diffusion method. Virulence factors were evaluated by multiplex PCR, and the clonal relationship among the resistant isolates was studied by Pulsed Field Gel Electrophoresis (PFGE). All isolates were susceptible to ceftriaxone. Overall, 26%, 20.2%, 15.4% and 6% of the isolates were resistant to tetracycline, ampicillin, sulfamethoxazole/trimethoprim and cephalotin, respectively. Twenty two percent of the isolates exhibited resistance to more than one antimicrobial agent. Multiple-drug resistance was mostly observed in the human isolates and involved the antibiotics ampicillin and tetracycline. None of the six virulence genes were identified among the isolates. Analysis of genetic diversity by PFGE of 31 resistant isolates, revealed 29 distinct restriction patterns. In conclusion, E. coli from humans and foods are resistant to commonly used antibiotics and are highly genetically diverse. In this setting, inappropriate use of antibiotics may be a cause of high resistance rate instead of clonal spread. PMID:26691477

  16. Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua.

    PubMed

    Rovira, Laia; Trobajo, Rosa; Sato, Shinya; Ibez, Carles; Mann, David G

    2015-01-01

    Nitzschia inconspicua is an ecologically important diatom species, which is believed to have a widespread distribution and to be tolerant to salinity and to organic or nutrient pollution. However, its identification is not straightforward and there is no information on genetic and ecophysiological diversity within the species. We used morphological, molecular (rbcL and LSU D1-D3), ecophysiological and reproductive data to investigate whether N. inconspicua constitutes a single species with a broad ecological tolerance or two or more cryptic species with shared or different ecological preferences. Molecular genetic data for clones from upstream and deltaic sites in the Ebro River basin (Catalonia, Spain) revealed seven N. inconspicua rbcL + LSU genotypes grouped into three major clades. Two of the clades were related to other Nitzschia and Denticula species, making N. inconspicua paraphyletic and suggesting the need for taxonomic revision. Most clones were observed to be automictic, exhibiting paedogamy, and so the biological species concept cannot be used to establish species boundaries. Although there were morphological differences among clones, we found no consistent differences among genotypes belonging to different clades, which are definable only through sequence data. Nevertheless, separating the genotypes could be important for ecological purposes because two different ecophysiological responses were encountered among them. PMID:26046925

  17. Genetic diversity among sea otter isolates of Toxoplasma gondii.

    PubMed

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

    2008-02-14

    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. PMID:18155841

  18. Genetic diversity of pestivirus isolates in cattle from Western Austria.

    PubMed

    Hornberg, Andrea; Fernndez, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Kfer, Josef; Schpf, Karl

    2009-03-30

    The genetic diversity of bovine viral diarrhoea virus (BVDV) isolates in infected cattle from Tyrol and Vorarlberg (Austria) was investigated. Blood samples were collected within the compulsory Austrian BVDV control programme during 2005 and 2006. The 5'-untranslated region (5'-UTR) and partially the N-terminal autoprotease (N(pro)) were amplified by one-step reverse transcriptase-polymerase chain reaction (RT-PCR) and the PCR products were subsequently sequenced. Phylogenetic analysis based on 5'-UTR and N(pro) sequences demonstrated that almost all isolates (307/310) were of the BVDV-1 genotype. They were clustered into eight different subtypes, here listed by their frequency of occurrence: BVDV-1h (143), BVDV-1f (79), BVDV-1b (41), BVDV-1d (28), BVDV-1e (6), BVDV-1a (4), BVDV-1g (3) and BVDV1-k (3). Two pestivirus isolates were typed as BVDV-2 and one isolate as BDV closely related to Gifhorn strain (BDV-3). Correlation among isolates could only be observed at the farm level, i.e., within a herd. However, no correlation between the genetic and geographical distances could be observed above the farm level. Because of the wide distribution of certain BVDV-1 subtypes and the low prevalence of herd-specific strains, a determination of tracing routes of infection was not possible. Furthermore, recombination events were not detected. PMID:19019571

  19. 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.

  20. Genetic relationships of five Indian horse breeds using microsatellite markers.

    PubMed

    Behl, R; Behl, J; Gupta, N; Gupta, S C

    2007-05-01

    The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.580.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's DA genetic distance of 0.071 and 0.186, respectively. In a Nei's DA genetic distances based neighbour joining dendrogram of these breeds and a Thoroughbred horse outgroup, the four pony breeds of Spiti, Bhutia, Manipuri and Zanskari clustered together and then with the Marwari breed. All the Indian breeds clustered independently from Thoroughbreds. The genetic relationships of Indian horse breeds to each other correspond to their geographical/environmental distribution. PMID:22444405

  1. Levels of genetic diversity vary dramatically between Blastocystis subtypes.

    PubMed

    Stensvold, C Rune; Alfellani, Mohammed; Clark, C Graham

    2012-03-01

    Blastocystis is a common single-celled parasite of humans and other animals comprising at least 13 genetically distinct small subunit ribosomal RNA lineages (subtypes (STs)). In this study we investigated intra-subtype genetic diversity and host specificity of two of the most common subtypes in humans, namely ST3 and ST4, by analysing and comparing over 400 complete and partial nuclear SSU-rDNAs and data from multilocus sequence typing (MLST) of the mitochondrion-like organelle (MLO) genome of 132 samples. Inferences from phylogenetic analyses of nuclear SSU-rDNA and concatenated MLST sequences were compatible. Human ST3 infections were restricted to one of four identified MLO clades except where exposure to non-human primates had occurred. This suggests relatively high host specificity within ST3, that human ST3 infections are caused predominantly by human-to-human transmission, and that human strains falling into other clades are almost certainly the result of zoonotic transmission. ST4 from humans belonged almost exclusively to one of two SSU-rDNA clades, and only five MLST sequence types were found among 50 ST4s belonging to Clade 1 (discriminatory index: 0.41) compared to 58 MLST sequence types among 81 ST3s (discriminatory index: 0.99). The remarkable differences in intra-subtype genetic variability suggest that ST4 has a more recent history of colonising humans than ST3. This is congruent with the apparently restricted geographical distribution of ST4 relative to ST3. The implications of this observation are unclear, however, and the population structure and distribution of ST4 should be subject to further scrutiny in view of the fact ST4 is being increasingly linked with intestinal disease. PMID:22116021

  2. SSRs transferability and genetic diversity of three allogamous ryegrass species.

    PubMed

    Guo, Zhi-Hui; Fu, Kai-Xin; Zhang, Xin-Quan; Zhang, Cheng-Lin; Sun, Ming; Huang, Ting; Peng, Yan; Huang, Lin-Kai; Yan, Yan-Hong; Ma, Xiao

    2016-02-01

    Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, and high repeatability. However, microsatellites are not always available for the species to be studied and their isolation could be time- and cost-consuming. To investigate transferability in cross-species applications, 102 primer pairs previously developed in ryegrass and tall fescue were amplified across three allogamous ryegrass species including Loliumrigidum, Lolium perenne and Lolium multiflorum. Their highly transferability (100%) were evidenced. While, most of these markers were multiple loci, only 17 loci were selected for a robust, single-locus pattern, which may be due to the recentness of the genome duplication or duplicated genomic regions, as well as speciation. A total of 87 alleles were generated with an average of 5.1 per locus. The mean polymorphism information content (PIC) and observed heterozygosity (Ho) values at genus was 0.5532 and 0.5423, respectively. Besides, analysis of molecular variance (AMOVA) revealed that all three levels contributed significantly to the overall genetic variation, with the species level contributing the least (P<0.001). Also, the unweighted pair group method with arithmetic averaging dendrogram (UPGMA), Bayesian model-based STRUCTURE analysis and the principal coordinate analysis (PCoA) showed that accessions within species always tended to the same cluster firstly and then to related species. The results showed that these markers developed in related species are transferable efficiently across species, and likely to be useful in analyzing genetic diversity. PMID:26874459

  3. Global relationship between phytoplankton diversity and productivity in the ocean

    PubMed Central

    Vallina, S. M.; Follows, M. J.; Dutkiewicz, S.; Montoya, J. M.; Cermeno, P.; Loreau, M.

    2014-01-01

    The shape of the productivitydiversity relationship (PDR) for marine phytoplankton has been suggested to be unimodal, that is, diversity peaking at intermediate levels of productivity. However, there are few observations and there has been little attempt to understand the mechanisms that would lead to such a shape for planktonic organisms. Here we use a marine ecosystem model together with the community assembly theory to explain the shape of the unimodal PDR we obtain at the global scale. The positive slope from low to intermediate productivity is due to grazer control with selective feeding, which leads to the predator-mediated coexistence of prey. The negative slope at high productivity is due to seasonal blooms of opportunist species that occur before they are regulated by grazers. The negative side is only unveiled when the temporal scale of the observation captures the transient dynamics, which are especially relevant at highly seasonal latitudes. Thus selective predation explains the positive side while transient competitive exclusion explains the negative side of the unimodal PDR curve. The phytoplankton community composition of the positive and negative sides is mostly dominated by slow-growing nutrient specialists and fast-growing nutrient opportunist species, respectively. PMID:24980772

  4. Global relationship between phytoplankton diversity and productivity in the ocean.

    PubMed

    Vallina, S M; Follows, M J; Dutkiewicz, S; Montoya, J M; Cermeno, P; Loreau, M

    2014-01-01

    The shape of the productivity-diversity relationship (PDR) for marine phytoplankton has been suggested to be unimodal, that is, diversity peaking at intermediate levels of productivity. However, there are few observations and there has been little attempt to understand the mechanisms that would lead to such a shape for planktonic organisms. Here we use a marine ecosystem model together with the community assembly theory to explain the shape of the unimodal PDR we obtain at the global scale. The positive slope from low to intermediate productivity is due to grazer control with selective feeding, which leads to the predator-mediated coexistence of prey. The negative slope at high productivity is due to seasonal blooms of opportunist species that occur before they are regulated by grazers. The negative side is only unveiled when the temporal scale of the observation captures the transient dynamics, which are especially relevant at highly seasonal latitudes. Thus selective predation explains the positive side while transient competitive exclusion explains the negative side of the unimodal PDR curve. The phytoplankton community composition of the positive and negative sides is mostly dominated by slow-growing nutrient specialists and fast-growing nutrient opportunist species, respectively. PMID:24980772

  5. Land use, genetic diversity and toxicant tolerance in natural populations of Daphnia magna.

    PubMed

    Coors, Anja; Vanoverbeke, Joost; De Bie, Tom; De Meester, Luc

    2009-10-19

    Provided that gene flow is not too high, selection by local environmental conditions in heterogeneous landscapes can lead to genetic adaptation of natural populations to their local habitat. Pollution with anthropogenic toxicants may create pronounced environmental gradients that impose strong local selection pressures. Toxic contaminants may also directly impact genetic structure in natural populations by exhibiting genotoxicity or by causing population declines resulting in genetic bottlenecks. Using populations of Daphnia magna established from the dormant egg banks of ponds located in a landscape dominated by anthropogenic impact, we aimed at detecting evidence for local adaptation to environmental contamination. We explored the relationship between land use around the 10 investigated ponds, population genetic diversity as measured by neutral genetic markers (polymorphic allozymes) and the tolerance of the populations originating from these ponds to acute lethal effects of two model toxicants, the pesticide carbaryl and the metal potassium dichromate. Genetic diversity of the populations as observed by neutral markers tended to be negatively impacted by agricultural land use intensity (Spearman rank correlation, R=-0.614, P=0.059), indicating that genetic bottlenecks may have resulted from anthropogenic impact. We experimentally observed differences in susceptibility to both carbaryl and potassium dichromate among the studied pond populations of D. magna (analysis of deviance, P<0.001). Because the experimental design excluded the possibility of physiological adaptation of the test animals to the toxicants, we conclude that the differences in susceptibility must have a genetic basis. Moreover, carbaryl tolerance levels of the populations tended to increase with increasing agricultural land use intensity as described by ranked percentage of land coverage with cereal and corn crop in the proximity of the ponds (Spearman rank correlation, R=0.602, P=0.066). Together, these two findings provide evidence for local adaptation of D. magna populations to pesticide contamination. Overall, the results demonstrate the potential selection pressure imposed by anthropogenic pollution and provide evidence that genetic erosion in natural Daphnia populations is related to anthropogenic impact. PMID:19747740

  6. 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. PMID:25060951

  7. High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

    PubMed Central

    Barry, Alyssa E.; Schultz, Lee; Senn, Nicholas; Nale, Joe; Kiniboro, Benson; Siba, Peter M.; Mueller, Ivo; Reeder, John C.

    2013-01-01

    High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity. PMID:23400571

  8. What is the genetic relationship between anxiety and depression?

    PubMed

    Hettema, John M

    2008-05-15

    Anxiety and depression share a long, close history in psychiatric nosology and treatment. The anxiety disorders, individually and as a group, exhibit remarkably high rates of comorbidity with each other and with major depression. Analyses done in large-scale epidemiologic surveys have identified major patterns of phenomenological overlap between these conditions. Researchers have tested hypotheses of shared genetic etiologies as a potential basis of this relationship. In general, available family studies have found mixed evidence for co-aggregation of anxiety and depressive disorders, while twin studies more definitively indicate that shared genetic risk factors largely account for this comorbidity. Some of this appears to be accounted for by genetic variation in personality traits that broadly predispose to anxiety and depression. Molecular genetic studies of these conditions, though too early to draw firm conclusions, thus far provide tentative support for specific genetic loci that may generally influence susceptibility across the anxiety-depressive spectrum. PMID:18412101

  9. Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity.

    PubMed

    Warner, Patricia A; van Oppen, Madeleine J H; Willis, Bette L

    2015-06-01

    Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within-species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population-level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G"ST ) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G"ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species. PMID:25943487

  10. Microsatellite diversity reveals the interplay of language and geography in shaping genetic differentiation of diverse Proto-Australoid populations of west-central India.

    PubMed

    Gaikwad, Sonali; Vasulu, T S; Kashyap, V K

    2006-02-01

    Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations. PMID:16323197

  11. Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae).

    PubMed

    Palop-Esteban, M; Segarra-Moragues, J G; Gonzlez-Candelas, F

    2007-09-01

    Microsatellite markers were used to evaluate the genetic diversity and population genetic structure in the critically endangered Limonium dufourii (Plumbaginaceae), a highly endemic triploid species from the coasts of eastern Spain. Sixty-five alleles from 13 microsatellite regions were amplified in a sample of 122 individuals collected from the six extant populations. Microsatellite patterns were consistent with the triploid nature of L. dufourii. Alleles were unambiguously assigned to two different parental subgenomes in this hybrid species and the greater contribution of the diploid parental subgenome was confirmed. Eleven, 25 and 26 multilocus genotypes were recorded from the haploid, diploid and from the combined information of both subgenomes, respectively. Genetic diversity was mostly distributed among populations (72.06% of the total genetic variation). Genotypes from Marjal del Moro populations grouped into two highly structured clusters (88.41% of the total variance). The observed patterns of distribution of genetic diversity are interpreted to result from multiple hybridization events and isolation between populations. Threats to this species are mainly anthropogenic (urbanization and tourism pressure), although stochastic risks cannot be ignored. Therefore, in order to preserve extant genetic variation of L. dufourii, in situ strategies such as the preservation of its habitat are a high priority. Several recommendations in order to assist ex situ measures to guarantee the success of conservation strategies and maintain the relationships between individuals and populations are proposed. PMID:17850548

  12. Genetic diversity between the Angus, the American Brahman, the Senepol, and the Romosinuano cattle breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to quantify the genetic diversity among the breeds under evaluation at the USDA, ARS, Subtropical Agricultural Research Station (STARS). Twenty-six microsatellite loci were used to estimate parameters of genetic diversity among a Bos indicus breed, Brahman (B), and t...

  13. How do reproductive skew and founder group size affect genetic diversity in reintroduced populations?

    PubMed

    Miller, K A; Nelson, N J; Smith, H G; Moore, J A

    2009-09-01

    Reduced genetic diversity can result in short-term decreases in fitness and reduced adaptive potential, which may lead to an increased extinction risk. Therefore, maintaining genetic variation is important for the short- and long-term success of reintroduced populations. Here, we evaluate how founder group size and variance in male reproductive success influence the long-term maintenance of genetic diversity after reintroduction. We used microsatellite data to quantify the loss of heterozygosity and allelic diversity in the founder groups from three reintroductions of tuatara (Sphenodon), the sole living representatives of the reptilian order Rhynchocephalia. We then estimated the maintenance of genetic diversity over 400 years (approximately 10 generations) using population viability analyses. Reproduction of tuatara is highly skewed, with as few as 30% of males mating across years. Predicted losses of heterozygosity over 10 generations were low (1-14%), and populations founded with more animals retained a greater proportion of the heterozygosity and allelic diversity of their source populations and founder groups. Greater male reproductive skew led to greater predicted losses of genetic diversity over 10 generations, but only accelerated the loss of genetic diversity at small population size (<250 animals). A reduction in reproductive skew at low density may facilitate the maintenance of genetic diversity in small reintroduced populations. If reproductive skew is high and density-independent, larger founder groups could be released to achieve genetic goals for management. PMID:19732338

  14. GENETIC DIVERSITY AMONG THE ANGUS, THE AMERICAN BRAHMAN, THE SENEPOL AND THE ROMOSINUANO CATTLE BREEDS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to quantify the genetic diversity among the breeds for tropical adaptability traits affecting the performance of beef cattle in the southern United States. Twenty-six microsatellite loci were used to estimate parameters of genetic diversity among a Bos indicus breed,...

  15. 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...

  16. Preliminary assessment of genetic diversity of Italian honey bees in the USA and Italy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Declining numbers of breeder queens and the concomitant loss of genetic diversity potentially could result in inbreeding and increased susceptibility to pests and disease in honey bees. Genetic diversity of commercial Italian bee colonies in the United States and Italy was assessed using microsatell...

  17. 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...

  18. 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. PMID:26663614

  19. Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands.

    PubMed

    Raffl, C; Holderegger, R; Parson, W; Erschbamer, B

    2008-05-01

    How does genetic diversity within populations of plants develop during primary succession on alpine glacier forelands? Theory predicts that pioneer populations are characterized by low genetic diversity due to founder effects and that genetic diversity increases within populations as they mature and recurrent gene flow occurs. However, few genetic studies have so far been carried out on plants on glacier forelands. In this study, we analysed the development of genetic diversity with time for populations of Trifolium pallescens along successional series (chronosequences) on three parallel glacier forelands in the European Alps, using neutral amplified fragment length polymorphism. No general trend in the development of genetic diversity was observed with increasing population age: even pioneer populations harboured substantial genetic diversity. Assignment tests showed that the latter consist of a genetic sub-sample from several source areas, and not just from other populations on the glacier forelands. We also detected some long distances-that is, inter-valley gene flow events. However, gene flow was not spatially unrestricted, as shown by a weak isolation by distance pattern within glacier valleys. The actual patterns of genetic diversity along the chronosequences are a result of the combination of factors, such as gene flow and growth rate, influenced by site- and species-specific attributes. PMID:18270530

  20. Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting.

    PubMed

    He, G; Prakash, C S; Jarret, R L

    1995-10-01

    A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base. PMID:8537002

  1. Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach

    PubMed Central

    Pascual, Laura; Xu, Jiaxin; Causse, Mathilde

    2013-01-01

    Integrative systems biology proposes new approaches to decipher the variation of phenotypic traits. In an effort to link the genetic variation and the physiological and molecular bases of fruit composition, the proteome (424 protein spots), metabolome (26 compounds), enzymatic profile (26 enzymes), and phenotypes of eight tomato accessions, covering the genetic diversity of the species, and four of their F1 hybrids, were characterized at two fruit developmental stages (cell expansion and orange-red). The contents of metabolites varied among the genetic backgrounds, while enzyme profiles were less variable, particularly at the cell expansion stage. Frequent genotype by stage interactions suggested that the trends observed for one accession at a physiological level may change in another accession. In agreement with this, the inheritance modes varied between crosses and stages. Although additivity was predominant, 40% of the traits were non-additively inherited. Relationships among traits revealed associations between different levels of expression and provided information on several key proteins. Notably, the role of frucktokinase, invertase, and cysteine synthase in the variation of metabolites was highlighted. Several stress-related proteins also appeared related to fruit weight differences. These key proteins might be targets for improving metabolite contents of the fruit. This systems biology approach provides better understanding of networks controlling the genetic variation of tomato fruit composition. In addition, the wide data sets generated provide an ideal framework to develop innovative integrated hypothesis and will be highly valuable for the research community. PMID:24151307

  2. High genetic diversity in the remnant island population of hihi and the genetic consequences of re-introduction.

    PubMed

    Brekke, Patricia; Bennett, Peter M; Santure, Anna W; Ewen, John G

    2011-01-01

    The maintenance of genetic diversity is thought to be fundamental for the conservation of threatened species. It is therefore important to understand how genetic diversity is affected by the re-introduction of threatened species. We use establishment history and genetic data from the remnant and re-introduced populations of a New Zealand endemic bird, the hihi Notiomystis cincta, to understand genetic diversity loss and quantify the genetic effects of re-introduction. Our data do not support any recent bottleneck events in the remnant population. Furthermore, all genetic diversity measures indicate the remnant hihi population has retained high levels of genetic diversity relative to other New Zealand avifauna with similar histories of decline. Genetic diversity (N(A) , alleles per locus, allelic richness, F(IS) and H(S) ) did not significantly decrease in new hihi populations founded through re-introduction when compared to their source populations, except in the Kapiti Island population (allelic richness and H(S) ) which had very slow post-re-introduction population growth. The N(e) /N(c) ratio in the remnant population was high, but decreased in first-level re-introductions, which together with significant genetic differentiation between populations (F(ST) & Fisher's exact tests) suggest that extant populations are diverging as a result of founder effects and drift. Importantly, simulations of future allele loss predict that the number of alleles lost will be higher in populations with a slow population growth, fewer founding individuals and with nonrandom mating. Interestingly, this species has very high levels of extra-pair paternity which may reduce reproductive variance by allowing social and floater males to reproduce a life history trait that together with a large remnant population size may help maintain higher levels of genetic diversity than expected. PMID:21073589

  3. Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere.

    PubMed

    Tian, Fang; Ding, Yanqin; Zhu, Hui; Yao, Liangtong; Du, Binghai

    2009-04-01

    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 ?-, ?-, ?-Proteobacteria, Sphingobacteria, Bacilli, and Actinobacteria. Especially, ?-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

  4. 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.

  5. 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, ?-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

  6. Gut microbiology - broad genetic diversity, yet specific metabolic niches.

    PubMed

    John Wallace, R

    2008-05-01

    Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability. PMID:22443591

  7. GENETIC RELATIONSHIPS AMONG FERTILITY TRAITS OF HOLSTEINS AND JERSEYS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dairy Herd Improvement data with service dates from 2,195,643 Holstein and 171,981 Jersey sire-identified lactations from 1995 through 2000 were used to assess genetic variation in and relationships among fertility traits: days to first service (D1), days to last reported service (DL), nonreturn rat...

  8. Intracolonial genetic diversity in honey bee (Apis mellifera) colonies increases pollen foraging efficiency

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiple mating by honey bee queens results in colonies of genotypically diverse workers. Recent studies have demonstrated that increased genetic diversity within a honey bee colony increases the variation in the frequency of tasks performed by workers. We show that genotypically diverse colonies, ...

  9. Prevalence and Genetic Diversity of Coronaviruses in Bats from China

    PubMed Central

    Tang, X. C.; Zhang, J. X.; Zhang, S. Y.; Wang, P.; Fan, X. H.; Li, L. F.; Li, G.; Dong, B. Q.; Liu, W.; Cheung, C. L.; Xu, K. M.; Song, W. J.; Vijaykrishna, D.; Poon, L. L. M.; Peiris, J. S. M.; Smith, G. J. D.; Chen, H.; Guan, Y.

    2006-01-01

    Coronaviruses can infect a variety of animals including poultry, livestock, and humans and are currently classified into three groups. The interspecies transmissions of coronaviruses between different hosts form a complex ecosystem of which little is known. The outbreak of severe acute respiratory syndrome (SARS) and the recent identification of new coronaviruses have highlighted the necessity for further investigation of coronavirus ecology, in particular the role of bats and other wild animals. In this study, we sampled bat populations in 15 provinces of China and reveal that approximately 6.5% of the bats, from diverse species distributed throughout the region, harbor coronaviruses. Full genomes of four coronavirues from bats were sequenced and analyzed. Phylogenetic analyses of the spike, envelope, membrane, and nucleoprotein structural proteins and the two conserved replicase domains, putative RNA-dependent RNA polymerase and RNA helicase, revealed that bat coronaviruses cluster in three different groups: group 1, another group that includes all SARS and SARS-like coronaviruses (putative group 4), and an independent bat coronavirus group (putative group 5). Further genetic analyses showed that different species of bats maintain coronaviruses from different groups and that a single bat species from different geographic locations supports similar coronaviruses. Thus, the findings of this study suggest that bats may play an integral role in the ecology and evolution of coronaviruses. PMID:16840328

  10. Bartonella prevalence and genetic diversity in small mammals from Ethiopia.

    PubMed

    Meheretu, Yonas; Leirs, Herwig; Welegerima, Kiros; Breno, Matteo; Tomas, Zewdneh; Kidane, Dawit; Girmay, Kokob; de Bellocq, Joëlle Goüy

    2013-03-01

    More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals was 34.0%. The probability of Bartonella infection varied significantly with species, sex, sexual condition, and some locality, but not with season, elevation, habitat type, animal weight, and ectoparasite infestation. In total, we found 18 unique Bartonella genotypes clustered into 5 clades, 1 clade exclusively Ethiopian, 2 clades clustered with genotypes from central and eastern Africa, and the remaining 2 clades clustered with genotypes and species from Africa and Asia. The close relatedness of several of our Bartonella genotypes obtained from the 3 dominant rodent species in Tigray with the pathogenic Bartonella elizabethae from Rattus spp. in Asia indicates a potential public health threat. PMID:23421888

  11. Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity

    PubMed Central

    Mller, 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 secondnineteenth 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 eighteenthnineteenth 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

  12. Exhaustive search for conservation networks of populations representing genetic diversity.

    PubMed

    Diniz-Filho, J A F; Diniz, J V B P L; Telles, M P C

    2016-01-01

    Conservation strategies routinely use optimization methods to identify the smallest number of units required to represent a set of features that need to be conserved, including biomes, species, and populations. In this study, we provide R scripts to facilitate exhaustive search for solutions that represent all of the alleles in networks with the smallest possible number of populations. The script also allows other variables to be added to describe the populations, thereby providing the basis for multi-objective optimization and the construction of Pareto curves by averaging the values in the solutions. We applied this algorithm to an empirical dataset that comprised 23 populations of Eugenia dysenterica, which is a tree species with a widespread distribution in the Cerrado biome. We observed that 15 populations would be necessary to represent all 249 alleles based on 11 microsatellite loci, and that the likelihood of representing all of the alleles with random networks is less than 0.0001. We selected the solution (from two with the smallest number of populations) obtained for the populations with a higher level of climatic stability as the best strategy for in situ conservation of genetic diversity of E. dysenterica. The scripts provided in this study are a simple and efficient alternative to more complex optimization methods, especially when the number of populations is relatively small (i.e., <25 populations). PMID:26909939

  13. 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. PMID:25988829

  14. Prevalence and genetic diversity of bovine kobuvirus in China.

    PubMed

    Chang, Jitao; Wang, Qian; Wang, Fang; Jiang, Zhigang; Liu, Yue; Yu, Li

    2014-06-01

    A total of 166 faecal specimens from diarrheic cattle were collected in China for detection of bovine kobuvirus (BKV) by reverse transcription PCR (RT-PCR) targeting the region a portion of the 3D nonstructural protein, with an amplicon size of 631 bp. The RNA corresponding to the BKV 3D region was detected in 34.9 % of faecal samples (58/166) in four major dairy-cattle-production areas in China, and sequence analysis based on the partial 3D sequences (35/58) indicated that the Chinese BKVs shared 88.9-96.2 % nucleotide sequence identity to BKV reference strains. Further phylogenetic analysis based on the complete VP1-encoding sequences (17/35) revealed that the Chinese BKVs shared 81-83.4 % nucleotide sequence identity to the U-1 strain, and these Chinese BKV strains, together with the U-1 strain, are apparently divided into four lineages, representing four genotypes of BKV, designated as A, B, C and D. Our results show that BKV infection is widely distributed, with high genetic diversity in China. PMID:24366549

  15. Genetic diversity of Chlamydia among captive birds from central Argentina.

    PubMed

    Frutos, Mara C; Monetti, Marina S; Vaulet, Lucia Gallo; Cadario, Mara E; Fermepin, Marcelo Rodrguez; R, 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. PMID:25469538

  16. Genetic Diversity and the Reproductive System in Related Species of Antirrhinum

    PubMed Central

    MATEU-ANDRS, I.; DE PACO, L.

    2006-01-01

    Background and Aims Seven related species of Antirrhinum (A. siculum, A. majus, A. latifolium, A. linkianum, A. litigiosum, A. cirrhigherum and A. tortuosum) were studied in order to compare levels of genetic variation and its partitioning in them, and to check relationships between genetic patterns and the reproductive system. Methods Eight hundred and fifty-one plants were screened for variability at 13 allozyme loci by means of horizontal starch gel electrophoresis. Parameters of genetic diversity and its partitioning, the inbreeding coefficient as well as an indirect estimate of gene flow based on the equation: Nm = (1 ? GST)/4GST, were calculated. Key Results Genetic variability in A. siculum was found to be the lowest known in the genus. Mean values of FIT and FIS were mostly positive and not significantly different from zero. Population differentiation (FST) ranged between 61 in A. tortuosum and 176 in A. linkianum. The inbreeding coefficient within populations ranged between FIS = ?05 in A. tortuosum and FIS = 1 in A. siculum. Estimates of gene flow ranged between Nm = 15 in A. majus (considered as very high) to Nm = 042 in A. siculum (considered as low). Conclusions Correlation was found between levels of diversity and differentiation on one hand, and the reproductive system of the studied taxa on the other. Striking differences among species in the inbreeding coefficient (FIS) show different reproductive systems, which mostly support previous reports. Strategies for the conservation of A. siculum are recommended, such as preservation of natural populations as well as ex situ preservation of seeds from different populations. PMID:17008348

  17. 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

  18. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    PubMed

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24%) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  19. Analysis of genetic diversity identified by amplified fragment length polymorphism marker in hybrid wheat.

    PubMed

    Ejaz, M; Qidi, Z; Gaisheng, Z; Na, N; Huiyan, Z; Qunzhu, W

    2015-01-01

    Amplified fragment length polymorphism markers were used to assess genetic diversity in 10 male sterile wheat crop lines (hetero-cytoplasm with the same nucleus) in relation to a restorer wheat line. These male sterile lines were evaluated using 64 amplified fragment length polymorphism primer combinations, and 13 primers produced polymorphic bands, generating a total 682 fragments. Of the 682 fragments, 113 were polymorphic. The polymorphic information content and marker index values demonstrated the utility of the primer combinations used in the present study. Unweighted pair group method with arithmetic mean and principal coordinate analysis of the genotypic data revealed clustering of accessions based on genetic relationships, and accessions were separated into 2 groups with their restorer line. Jaccard's similarity coefficient values suggested good variability among the male sterile lines, indicating their utility in breeding programs. The fallouts of analysis of molecular variance showed large within-group population variation, accounting for 77% of variation, while among-group comparison accounted for 23% of the total molecular variation, which was statistically significant. The molecular diversity observed in this study will be useful for selecting appropriate accessions for plant improvement and hybridization through molecular-breeding approaches and for developing suitable conservation strategies. PMID:26345825

  20. Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites

    PubMed Central

    Razafinarivo, Norosoa J.; Guyot, Romain; Davis, Aaron P.; Couturon, Emmanuel; Hamon, Serge; Crouzillat, Dominique; Rigoreau, Michel; Dubreuil-Tranchant, Christine; Poncet, Valerie; De Kochko, Alexandre; Rakotomalala, Jean-Jacques; Hamon, Perla

    2013-01-01

    Background and Aims The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated. Methods Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species. Key Results Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity. Conclusions Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions. PMID:23275631

  1. Analysis of the genetic diversity of Chinese native Cannabis sativa cultivars by using ISSR and chromosome markers.

    PubMed

    Zhang, L G; Chang, Y; Zhang, X F; Guan, F Z; Yuan, H M; Yu, Y; Zhao, L J

    2014-01-01

    Hemp (Cannabis sativa) is an important fiber crop, and native cultivars exist widely throughout China. In the present study, we analyzed the genetic diversity of 27 important Chinese native hemp cultivars, by using inter-simple sequence repeats (ISSR) and chromosome markers. We determined the following chromosome formulas: 2n = 20 = 14m + 6sm; 2n = 20 = 20m; 2n = 20 = 18m + 2sm; 2n = 20 = 16m + 4sm; and 2n = 20 = 12m + 8sm. The results of our ISSR analysis revealed the genetic relationships among the 27 cultivars; these relationships were analyzed by using the unweighted pair-group method based on DNA polymorphism. Our results revealed that all of the native cultivars showed considerable genetic diversity. At a genetic distance of 0.324, the 27 varieties could be classified into five categories; this grouping corresponded well with the chromosome formulas. All of the investigated hemp cultivars represent relatively primitive types; moreover, the genetic distances show a geographical distribution, with a small amount of regional hybridity. PMID:25511032

  2. MULTILOCUS SIMPLE SEQUENCE REPEATS AND SINGLE NUCLEOTIDE POLYMORPHISM MARKERS FOR GENOTYPING AND ASSESSING GENETIC DIVERSITY OF XYLELLA FASTIDIOSA IN CALIFORNIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To develop effective disease management strategies, we need to understand population structure and genetic diversity of pathogens in agricultural ecosystems. Current information regarding population structure and genetic diversity of Xylella fastidiosa (Xf) in California is insufficient to adequate...

  3. Genetic diversity of the bacterial wilt pathogen Ralstonia solanacearum using a RAPD marker.

    PubMed

    Nishat, Sayeda; Hamim, Islam; Khalil, M Ibrahim; Ali, Md Ayub; Hossain, Muhammed Ali; Meah, M Bahadur; Islam, Md Rashidul

    2015-11-01

    Bacterial wilt caused by Ralstonia solanacearum is a destructive disease of many economically important crop species. A significant variation in wilt incidence and severity in eggplant and potato was observed among the growing areas surveyed. R. solanacearum isolates obtained both from eggplant and potato belong to biovar III, while isolates from eggplant belong to race 1 and isolates obtained from potato belong to race 3. Random amplified polymorphic DNA (RAPD) technique was used as a tool for assessing genetic variation and relationship among seven isolate groups of R. solanacearum viz., RsB-1, RsB-2, RsB-3, RsP-1, RsP-2, RsP-3 and RsP-4, consisting in a total of 28 isolates. Out of the RAPD markers used, amplification with four decamer primers produced 70 bands with sizes ranging from 100 to 1400 bp. Out of 70 bands, 68 bands (97.06%) were polymorphic and two bands (2.94%) were monomorphic amongst the seven R. solanacearum isolates group. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's genetic distance produced two main clusters of the seven isolates of R. solanacearum. The isolates RsB-1, RsB-2, RsB-3 and R-4 grouped in cluster І, while RsP-2, RsP-3 and RsP-4 grouped in cluster ІІ. The highest intra-variety similarity index (Si) was found in RsB-1 isolate (86.35%) and the lowest one in RsP-2 (56.59%). The results indicated that relatively higher and lower levels of genetic variation were found in RsP-3 and RsB-3, respectively. The coefficient of gene differentiation (G(st)) was 0.5487, reflecting the existence of a high level of genetic variations among seven isolates of R. solanacearum. Comparatively higher genetic distance (0.4293) and lower genetic identity (0.6510) were observed between RsB-2 and RsP-4 combinations. The lowest genetic distance (0.0357) and highest genetic identity (0.9650) were found in RsB-1 vs. RsB-2 pair. Thus, RAPD offers a potentially simple, rapid and reliable method to evaluate genetic diversity analysis in R. solanacearum. PMID:26302834

  4. Genetic Diversity of Five Local Swedish Chicken Breeds Detected by Microsatellite Markers

    PubMed Central

    Abebe, Abiye Shenkut; Mikko, Sofia; Johansson, Anna M.

    2015-01-01

    This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshna, Hedemorahna, lndsk dvrghna, Sknsk blommehna, and Bohusln- Dals svarthna, in the rest of the paper the shorter name Svarthna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthna and the highest scores for the Sknsk blommehna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Sknsk blommehna having the lowest and Svarthna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (FST) was 0.440, and the global inbreeding of individuals within breed (FIS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahna and lndsk dvrghna breeds in one cluster, and Gotlandshna and Svarthna breeds in the second cluster leaving the Sknsk blommehna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahna, Gotlandshna and Svarthna breeds forming their own distinct clusters, while lndsk dvrghna and Sknsk blommehna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens. PMID:25855978

  5. Prevalence, genetic diversity, and host range of tectiviruses among members of the Bacillus cereus group.

    PubMed

    Gillis, Annika; Mahillon, Jacques

    2014-07-01

    GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found. PMID:24795369

  6. Prevalence, Genetic Diversity, and Host Range of Tectiviruses among Members of the Bacillus cereus Group

    PubMed Central

    Gillis, Annika

    2014-01-01

    GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found. PMID:24795369

  7. Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations.

    PubMed Central

    Lum, J K; Cann, R L; Martinson, J J; Jorde, L B

    1998-01-01

    Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania. PMID:9683581

  8. 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.

  9. Genetic Diversity in Passiflora Species Assessed by Morphological and ITS Sequence Analysis

    PubMed Central

    Ramaiya, Shiamala Devi; Bujang, Japar Sidik; Zakaria, Muta Harah

    2014-01-01

    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level. PMID:25050402

  10. Genetic diversity in Passiflora species assessed by morphological and its sequence analysis.

    PubMed

    Ramaiya, Shiamala Devi; Bujang, Japar Sidik; Zakaria, Muta Harah

    2014-01-01

    This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level. PMID:25050402

  11. Genetic diversity of rhizobia nodulating lentil (Lens culinaris) in Bangladesh.

    PubMed

    Rashid, Md Harun-or; Schfer, Holger; Gonzalez, Javier; Wink, Michael

    2012-03-01

    In order to determine the bacterial diversity and the identity of rhizobia nodulating lentil in Bangladesh, we performed a phylogenetic analysis of housekeeping genes (16S rRNA, recA, atpD and glnII) and nodulation genes (nodC, nodD and nodA) of 36 bacterial isolates from 25 localities across the country. Maximum likelihood (ML) and Bayesian analyses based on 16S rRNA sequences showed that most of the isolates (30 out of 36) were related to Rhizobium etli and Rhizobium leguminosarum. Only these thirty isolates were able to re-nodulate lentil under laboratory conditions. The protein-coding housekeeping genes of the lentil nodulating isolates showed 89.1-94.8% genetic similarity to the corresponding genes of R. etli and R. leguminosarum. The same analyses showed that they split into three distinct phylogenetic clades. The distinctness of these clades from closely related species was also supported by high resolution ERIC-PCR fingerprinting and phenotypic characteristics such as temperature tolerance, growth on acid-alkaline media (pH 5.5-10.0) and antibiotic sensitivity. Our phylogenetic analyses based on three nodulation genes (nodA, nodC and nodD) and cross-inoculation assays confirmed that the nodulation genes are related to those of R. leguminosarum biovar viciae, but clustered in a distinct group supported by high bootstrap values. Thus, our multi-locus phylogenetic analysis, DNA fingerprinting and phenotypic characterizations suggest that at least three different clades are responsible for lentil nodulation in Bangladesh. These clades differ from the R. etli-R. leguminosarum group and may correspond to novel species in the genus Rhizobium. PMID:22280898

  12. Genetic diversity of noroviruses in raw and treated sewage water.

    PubMed

    van den Berg, Harold; Lodder, Willemijn; van der Poel, Wim; Vennema, Harry; de Roda Husman, Ana Maria

    2005-05-01

    Human noroviruses cause gastroenteritis in humans, leading to high virus loads in sewage. Norovirus concentrations in raw and treated sewage samples from two sewage treatment plants (STP) were studied, along with virus removal and genetic diversity. Over one year, the average norovirus concentrations in raw sewage were approximately 10(5) pcr detectable units (pdu) per liter compared with 10(3) pdu/l of treated sewage. Similar sewage treatment processes at STP-A and STP-B led to 2.7 and 2.0 log(10)-units of virus removal, respectively. In total, 11 different norovirus variants were detected in 49 out of 53 sewage samples, with up to four different norovirus strains in a single sewage sample. Along with GGI.6 Sindlesham and GGII.2 Melksham, the GGIIb variant was one of the most prevalent noroviruses in both raw and treated sewage. This strain emerged among populations in Europe in 2000 and 2001. Treated sewage containing 10(2)-10(3) norovirus pdu is discharged into the surface water. The use of such fecally contaminated surface waters for shellfish culture, drinking water production and recreational purposes poses a potential health risk. We showed the presence of multiple norovirus strains in raw and treated sewage, confirming the need to clone before sequencing the RT-PCR products. Exposure to multiple norovirus strains in sewage contaminated food or water may lead to the occurrence of norovirus recombinants, which may be more virulent and pathogenic than the norovirus strains already circulating in the population. PMID:15862452

  13. Molecular biology and genetic diversity of Rift Valley fever virus

    PubMed Central

    Ikegami, Tetsuro

    2013-01-01

    Rift Valley fever virus (RVFV), a member of the family Bunyaviridae, genus Phlebovirus, is the causative agent of Rift Valley fever (RVF), a mosquito-borne disease of ruminant animals and humans. The generation of a large sequence database has facilitated studies of the evolution and spread of the virus. Bayesian analyses indicate that currently circulating strains of RVFV are descended from an ancestral species that emerged from a natural reservoir in Africa when large-scale cattle and sheep farming were introduced during the 19th century. Viruses descended from multiple lineages persist in that region, through infection of reservoir animals and vertical transmission in mosquitoes, emerging in years of heavy rainfall to cause epizootics and epidemics. On a number of occasions, viruses from these lineages have been transported outside the enzootic region through the movement of infected animals or mosquitoes, triggering outbreaks in countries such as Egypt, Saudi Arabia, Mauritania and Madagascar, where RVF had not previously been seen. Such viruses could potentially become established in their new environments through infection of wild and domestic ruminants and other animals and vertical transmission in local mosquito species. Despite their extensive geographic dispersion, all strains of RVFV remain closely related at the nucleotide and amino acid level. The high degree of conservation of genes encoding the virion surface glycoproteins suggests that a single vaccine should protect against all currently circulating RVFV strains. Similarly, preservation of the sequence of the RNA-dependent RNA polymerase across viral lineages implies that antiviral drugs targeting the enzyme should be effective against all strains. Researchers should be encouraged to collect additional RVFV isolates and perform whole-genome sequencing and phylogenetic analysis, so as to enhance our understanding of the continuing evolution of this important virus. This review forms part of a series of invited papers in Antiviral Research on the genetic diversity of emerging viruses. PMID:22710362

  14. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    PubMed Central

    Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

    2013-01-01

    Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73?kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

  15. Genetic Strategies for Probing Conscientiousness and its Relationship to Aging

    PubMed Central

    South, Susan C.; Krueger, Robert F.

    2013-01-01

    Conscientiousness is an important trait for understanding healthy aging. The current paper addresses how behavioral and molecular genetics methodologies can aid in furthering explicating the link between conscientiousness and aspects of health and well-being in later life. We review the etiology of conscientiousness documented by both quantitative and molecular genetics methods. We also discuss the ways behavior genetics can be used to continue to help refine the concept of conscientiousness and to help identify points of etiological overlap between conscientiousness and healthy aging outcomes. Phenotypic research has established non-trivial associations between conscientiousness and important outcomes, but behavior genetic methods can determine what the causal (genetic and environmental) mechanisms are behind these relationships. An empirical example of one of these techniques is provided using twin data from the Midlife in the United States (MIDUS) study. We demonstrate that conscientiousness moderates genetic and environmental influences on problem alcohol use, such that greater levels of conscientiousness buffer against the random effects of the environment. Finally, suggestions for future work in this area are discussed. PMID:23181432

  16. Genetic relationship among reproductive traits in Nellore cattle.

    PubMed

    Guarini, A R; Neves, H H R; Schenkel, F S; Carvalheiro, R; Oliveira, J A; Queiroz, S A

    2015-05-01

    In order to achieve improvements in production efficiency in livestock, herds of high sexual precocity and good fertility are needed. These traits increase the availability of animals in herd, either for sale or selection, allowing both greater selective intensity and greater genetic progress. This study aimed at estimating genetic parameters for reproductive traits measured directly in females in order to verify whether they could be used as selection criteria for genetic improvement in Nellore cows, as well as estimating the genetic relationship among these traits and scrotal circumference (SC), the traditional selection criterion for sexual precocity in cattle. In addition to SC, stayability (STAY), number of calvings at 53 months (NC53) and heifers rebreeding (HR) were studied. The (co)variances and genetic parameters were estimated using Bayesian inference. STAY, NC53 and HR were analyzed assuming a threshold model, whereas SC was analyzed with a linear model. Heritability estimated for NC53 was 0.22, and this trait was strongly and positively correlated with STAY, meaning selection for NC53 would improve productive longevity of Nellore cows. Correlations estimated between HR and STAY (?0.97) and between HR and NC53 (?0.99) allow an improvement on HR rates if selection was applied to traits related to longevity. Genetic correlations among SC and female reproductive traits were positive but weak, suggesting the need to use reproductive traits directly measured in females in order to obtain greater improvements in sexual precocity and longevity. PMID:25483394

  17. 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. PMID:19765228

  18. Genetic diversity among toxigenic and nontoxigenic Vibrio cholerae O1 isolated from the Western Hemisphere.

    PubMed Central

    Chen, F.; Evins, G. M.; Cook, W. L.; Almeida, R.; Hargrett-Bean, N.; Wachsmuth, K.

    1991-01-01

    Multilocus enzyme electrophoresis was used to examine genetic relationships among and between toxigenic and non-toxigenic isolates of Vibrio cholerae O1 obtained from patients and the environment in the US Gulf Coast and surrounding areas. A total of 23 toxigenic and 23 non-toxigenic strains were examined. All the toxigenic and 7 of the non-toxigenic strains had the same alleles at 16 enzyme loci, whereas the balance of the nontoxigenic strains had 9 distinct combinations of alleles. This study suggests that all of the toxigenic strains belong to a single clone, and that while some of the non-toxigenic isolates were related, most were of diverse origin. PMID:1879486

  19. Using the Collaborative Cross to Study the Role of Genetic Diversity in Cancer-Related Phenotypes.

    PubMed

    Reilly, Karlyne M

    2016-01-01

    Human populations are genetically diverse and often a single mouse model can only represent a small subset of the human population. Studying genetic diversity directly can improve the predictive value of mouse models of cancer biology and research on the effects of carcinogens and therapeutics in humans. The collaborative cross is a panel of inbred mouse lines that captures 90% of the genetic diversity of the Mus musculus strain and can help identify regions of the genome that are responsible for variation in cancer phenotypes across the population. The appropriate procedure will depend on the mouse model used; here, three mouse cross designs are described as examples. PMID:26933242

  20. Relationships between Spatial Metrics and Plant Diversity in Constructed Freshwater Wetlands

    PubMed Central

    Grossman, Jake J.; Allen, George A.; Benzing, David H.

    2015-01-01

    The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland “cells” were constructed in former farmland in northeast Ohio. The systems were subjected to planting treatments that resulted in different levels of vascular plant species diversity among cells. Plant species diversity was assessed through annual inventories. Plant spatial pattern was assessed by digitizing low-altitude aerial photographs taken at the same time as the inventories. Diversity metrics derived from the inventories were significantly related to certain spatial metrics derived from the photographs, including cover type diversity and contagion. We found that wetlands with high cover type diversity harbor higher plant species diversity than wetlands with fewer types of patches. We also found significant relationships between plant species diversity and spatial patterning of patch types, but the direction of the effect differed depending on the diversity metric used. Links between diversity and spatial pattern observed in this study suggest that high-resolution aerial imagery may provide wetland scientists with a useful tool for assessing plant diversity. PMID:26296205

  1. 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

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

    PubMed

    Banhos, Aureo; Hrbek, Tomas; Sanaiotti, Tnia M; Farias, Izeni Pires

    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

  3. 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

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

    PubMed

    Bach, Lis; Dahllf, 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. PMID:22421731

  5. Life history influences how fire affects genetic diversity in two lizard species.

    PubMed

    Smith, Annabel L; Bull, C Michael; Gardner, Michael G; Driscoll, Don A

    2014-05-01

    'Fire mosaics' are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re-establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow i