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1

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

PubMed

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

Aguiar, G F

1991-12-01

2

Genetic Diversity and Relationships of Wheat Landraces from Oman Investigated with SSR Markers  

Microsoft Academic Search

Little is known about genetic diversity and geographic origin of wheat landraces from Oman, an ancient area of wheat cultivation. The objectives of this study were to investigate the genetic relationships and levels of diversity of six wheat landraces collected in Oman with a set of 30 evenly distributed SSR markers. The total gene diversity, (HT), conserved in the three

P. Zhang; S. Dreisigacker; A. Buerkert; S. Alkhanjari; A. E. Melchinger; M. L. Warburton

2006-01-01

3

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis  

PubMed Central

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

Whitlock, Raj

2014-01-01

4

Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum ( Malvaceae )  

Microsoft Academic Search

Gossypium mustelinum, one of five tetraploid species in the cotton genus, is geographically restricted to a few states in NE Brazil. Allozyme analysis was used to assess levels and patterns of genetic diversity inG. mustelinum and its relationship to the other tetraploid species. Genetic variation was low, with only 6 of 50 loci examined being polymorphic, a mean of 1.14

Jonathan F. Wendel; Robb Rowley; James Mc D. Stewart

1994-01-01

5

Genetic diversity and relationships of lotus ( Nelumbo) cultivars based on allozyme and ISSR markers  

Microsoft Academic Search

Genetic diversity and genetic relationships of lotus (Nelumbo Adanson) cultivars were evaluated using allozyme and ISSR markers. The samples used covered 11 accessions of possible hybrids between Nelumbo nucifera and Nelumbo lutea and 92 accessions of N. nucifera including 69 flower lotus, 13 rhizome lotus, 5 seed lotus and 5 wild lotus. For allozyme studies, a total of 31 alleles

Hong-Li Tian; Jian-Hua Xue; Jun Wen; Grant Mitchell; Shi-Liang Zhou

2008-01-01

6

Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection  

Microsoft Academic Search

A collection of 66 Malus?domestica Borkh. accessions from the USDA-ARS Plant Genetic Resources Unit’s core collection was screened with a set of eight SSR (simple\\u000a sequence repeat) primers developed at the PGRU in order to determine genetic identities, estimate genetic diversity, and to\\u000a identify genetic relationships among these accessions. All eight primer pairs generated multiple fragments when used in amplification

S. C. Hokanson; A. K. Szewc-McFadden; W. F. Lamboy; J. R. McFerson

1998-01-01

7

Genetic diversity and relationships of cacao (Theobroma cacao L.) in southern Mexico  

Microsoft Academic Search

Neotropical tree crops are affected by a combination of biological and human factors that complicate the study of genetic\\u000a diversity and crop evolution. Genetic diversity and relationships among southern Mexican populations and horticultural collections\\u000a of Theobroma cacao (chocolate, cocoa, cacao) are examined in light of the agricultural practices of the Maya. Collections of cacao were obtained\\u000a from the extremes of

R. Whitkus; M. de la Cruz; L. Mota-Bravo; A. Gómez-Pompa

1998-01-01

8

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers.  

PubMed

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources. PMID:25358313

Suh, Sangwon; Kim, Young-Sin; Cho, Chang-Yeon; Byun, Mi-Jeong; Choi, Seong-Bok; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Bae, Kyoung Hun; Kim, Jae-Hwan

2014-11-01

9

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers  

PubMed Central

Four Korean native cattle (KNC) breeds—Hanwoo, Chikso, Heugu, and Jeju black—are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources. PMID:25358313

Suh, Sangwon; Kim, Young-Sin; Cho, Chang-Yeon; Byun, Mi-Jeong; Choi, Seong-Bok; Ko, Yeoung-Gyu; Lee, Chang Woo; Jung, Kyoung-Sub; Bae, Kyoung Hun; Kim, Jae-Hwan

2014-01-01

10

Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers.  

PubMed

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

Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F

2014-01-01

11

Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers  

PubMed Central

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-01-01

12

Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers.  

PubMed

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds. PMID:25178290

Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

2014-10-01

13

Microsatellite Diversity Delineates Genetic Relationships of Shia and Sunni Muslim Populations of Uttar Pradesh, India  

Microsoft Academic Search

:In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317,

Muthukrishnan Eaaswarkhanth; Bhawna Dubey; Poorlin Ramakodi Meganathan; Sabahat Noor; Ikramul Haque

2009-01-01

14

Microsatellite Diversity Delineates Genetic Relationships of Shia and Sunni Muslim Populations of Uttar Pradesh, India  

Microsoft Academic Search

In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317,

2009-01-01

15

Genetic diversity and relationships among Dutch elm disease tolerant Ulmus pumila L. accessions from China.  

PubMed

Elm breeding programs worldwide have relied heavily on Asian elm germplasm, particularly Ulmus pumila, for the breeding of Dutch elm disease tolerant cultivars. However, the extent and patterning of genetic variation in Asian elm species is unknown. Therefore, the objective of this research was to determine the extent of genetic diversity among 53 U. pumila accessions collected throughout the People's Republic of China. Using 23 microsatellite loci recently developed in the genus Ulmus, a total of 94 alleles were identified in 15 polymorphic and 4 monomorphic loci. The average number of alleles per locus was 4.9, with a range of 1-11 alleles. Gene diversity estimates per locus ranged from 0.08 to 0.87, and the non-exclusion probability for the 15 polymorphic loci combined was 0.7 x 10(-9). Nineteen region-specific alleles were identified, and regional gene diversity estimates were moderately high (0.48-0.57). The genetic relationships among accessions and regions were estimated by UPGMA and principal coordinate analysis. Both techniques discriminated all accessions and regions. Two microsatellite markers (UR175 + UR123 or Ulm-3) were sufficient to discriminate up to 99.7% of the accessions studied. This research provides useful information for DNA-based fingerprinting, breeding, ecological studies, and diversity assessment of elm germplasm. PMID:18545273

Zalapa, Juan E; Brunet, Johanne; Guries, Raymond P

2008-07-01

16

No relationship between individual genetic diversity and prevalence of avian malaria in a migratory kestrel.  

PubMed

Insight into the genetic basis of malaria resistance is crucial for understanding the consequences of this parasite group on animal populations. Here, we analyse the relationship between genotypic variation at 11 highly variable microsatellite loci and prevalence of three different lineages of avian malaria, two Plasmodium (RTSR1, LK6) and one Haemoproteus (LK2), in a wild population of the endangered lesser kestrel (Falco naumanni). Although we used a large sample size (584 typed individuals), we did not find any significant association between the prevalence of the studied parasite lineages and individual genetic diversity. Although our data set is large, the 11 neutral markers typed may have had low power to detect such association, in part because of the low parasite prevalence observed (less than 5% of infected birds). However, the fact that we have detected previous correlations between genetic diversity and other traits (ectoparasitism risk, fecundity) in the study population using the same panel of neutral markers and lower sample sizes suggests that other factors could underlie the absence of such a similar correlation with avian malaria. Differences in the genetics of the studied traits and in their particular basis of inbreeding depression (dominance vs. overdominance) may have led to malaria prevalence, but not other traits, being uncoupled with individual genetic diversity. Also, we cannot discard the possibility that the absence of association was a consequence of a low pathogenic effect of these particular malaria lineages on our lesser kestrel population, and thus we should not expect the evolution of genetic resistance against these parasites. PMID:17944853

Ortego, Joaquín; Cordero, Pedro J; Aparicio, José Miguel; Calabuig, Gustau

2007-11-01

17

Genetic Diversity and Phylogenetic Relationships of Two Closely Related Northeast China Vicia Species Revealed with RAPD and ISSR Markers  

Microsoft Academic Search

RAPD and ISSR analyses revealed genetic diversity and relationships among 11 populations of two closely related northeast\\u000a China Vicia species, Vicia ramuliflora and V. unijuga. Both methods yielded similar and complementary results, showing high genetic diversity. Vicia ramuliflora had 100% polymorphic loci in both RAPD and ISSR, and V. unijuga had 100% polymorphic loci for RAPD and 98.96% for ISSR.

Ying Han; Hao-You Wang

2010-01-01

18

Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India.  

PubMed

In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations. PMID:20067368

Eaaswarkhanth, Muthukrishnan; Dubey, Bhawna; Ramakodi Meganathan, Poorlin; Noor, Sabahat; Haque, Ikramul

2009-08-01

19

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

PubMed Central

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

Simental-Rodriguez, Sergio Leonel; Quinones-Perez, Carmen Zulema; Moya, Daniel; Hernandez-Tecles, Enrique; Lopez-Sanchez, Carlos Antonio; Wehenkel, Christian

2014-01-01

20

Genetic diversity and relationships among accessions of five crested wheatgrass species (Poaceae: Agropyron) based on gliadin analysis.  

PubMed

Agropyron Gaertn. is the most important genus in Triticeae (Poaceae), which includes many forage grasses with high economic value. The genetic diversity and relationships of 36 accessions from five crested wheatgrass species were analyzed by gliadin markers. A total of 54 product bands were detected after acid polyacrylamide gel electrophoresis (A-PAGE), of which 100% were polymorphic. The genetic similarity coefficient based on Nei-Li's method ranged from 0.065 to 0.755 with an average of 0.451. The Shannon diversity information index showed that there was a high level of genetic diversity among the accessions. An unweighted pair group method with arithmetic average (UPGMA) dendrogram was constructed based on the Nei-Li's genetic similarity coefficients, which showed the phylogenetic relationships among accessions of different species. Analysis of molecular variance (AMOVA) showed that the proportion of variance explained by inter- and intraspecific variance was 9.34 and 90.66%, respectively, which revealed that the genetic variations within species were higher than the variations among species. Based on pairwise genetic distances (?ST) among species, the cluster analysis indicated that A. mongolicum had a low-affinity relationship with other species, while A. fragile showed a close relationship with A. cristatum ssp pectinatum. Finally, the implications of the results for the taxonomy of Agropyron were discussed. PMID:24301939

Chen, S Y; Ma, X; Zhang, X Q; Huang, L K; Zhou, J N

2013-01-01

21

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

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.

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

2014-01-01

22

Elucidating genetic relationships, diversity and population structure among the Turkish female figs  

Microsoft Academic Search

A collection of 96 female Turkish fig (Ficus carica L.) accessions was studied to elucidate genetic structure and estimate diversity and genetic similarity distribution among\\u000a the female figs present in Turkish genetic resources, using 157 molecular genome markers including 129 sequence-related amplified\\u000a polymorphisms, 21 random amplified polymorphic DNAs, and 7 simple-sequence repeats. The plant samples mainly included Turkish\\u000a fig collections

Hatice Ikten; Nedim Mutlu; Osman Gulsen; Hilmi Kocatas; Uygun Aksoy

2010-01-01

23

Genetic diversity and phylogenetic relationships of two closely related northeast China Vicia species revealed with RAPD and ISSR markers.  

PubMed

RAPD and ISSR analyses revealed genetic diversity and relationships among 11 populations of two closely related northeast China Vicia species, Vicia ramuliflora and V. unijuga. Both methods yielded similar and complementary results, showing high genetic diversity. Vicia ramuliflora had 100% polymorphic loci in both RAPD and ISSR, and V. unijuga had 100% polymorphic loci for RAPD and 98.96% for ISSR. Genetic differentiation was moderate among populations of each species. Genetic variation was distributed mainly within populations for the two species. The high level of gene flow was important for the allocation of genetic variation. The UPGMA dendrogram and principal coordinates analysis at the level of individuals and populations showed that V. ramuliflora and V. unijuga were more closely related than either of them was to the outgroup species, V. cracca. The small molecular variance of V. ramuliflora and V. unijuga supports the conclusion that these two species had a common ancestor. PMID:20039118

Han, Ying; Wang, Hao-You

2010-06-01

24

Genetic diversity among sapoviruses  

Microsoft Academic Search

Summary. Norovirus and Sapovirus are two genera of the family Caliciviridae that contain viruses that can cause acute gastroenteritis in humans. Noroviruses (NOR) are genetically highly diverse but limited studies of the genetic diversity of sapoviruses (SAP) have been reported. In this study we characterized twenty-five SAP detected in our laboratory from outbreaks or sporadic cases of acute gastroenteritis in

T. Farkas; W. M. Zhong; Y. Jing; P. W. Huang; S. M. Espinosa; N. Martinez; A. L. Morrow; G. M. Ruiz-Palacios; L. K. Pickering; X. Jiang

2004-01-01

25

Compromising Baltic salmon genetic diversity -  

E-print Network

Compromising Baltic salmon genetic diversity - conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea Havs- och vattenmyndighetens rapport 2012:18 #12;Compromising Baltic salmon genetic diversity - conservation genetic risks associated with compensatory releases

26

Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers  

PubMed Central

In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ?0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ?0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed. PMID:23518904

Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk

2013-01-01

27

Genetic diversity and evolutionary relationships of the troglodytic 'living fossil' Congeria kusceri (Bivalvia: Dreissenidae)  

Microsoft Academic Search

Population genetic theory predicts that long-term isolation of 'living fossils' in relic habitats might reduce genetic variability due to small population sizes and inbreeding. The recent description of a troglodytic 'living fossil' Congeria kusceri — the only known subterranean bivalve mollusc — from a genus thought to be extinct since the Miocene, offers a unique opportunity to examine this hypothesis.

C. A. S TEPIEN; B. M ORTON; K. A. D ABROWSKA; R. A. G UARNERA; T. R ADJA

28

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...

29

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

PubMed

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

Rocañín-Arjó, Ares; Rodríguez-Botigué, Laura; Esteban, Esther; Theves, Catherine; Evdokimova, Larissa E; Fedorova, Sardana A; Gibert, Morgane; Crubezy, Eric; Moral, Pedro

2013-01-01

30

Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae  

Microsoft Academic Search

Allelic polymorphism at the S locus that determines the gametophytic self-incompatibility (GSI) system in the pistil predates speciation. Understanding the evolution of a GSI system therefore requires knowledge of how lineage sorting and interspecific phylogenetic relationship affect S allele polymorphism. In searching for patterns of lineage sorting among species of various phylogenetic relationships, 22 S-alleles from 34 genets randomly taken

Yingqing Lu

2001-01-01

31

Genetic Diversity among Enterococcus faecalis  

PubMed Central

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

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

2007-01-01

32

Relationships between Population Size, Genetic Diversity and Fitness Components in the Rare Plant Dictamnus albus in Central Germany  

Microsoft Academic Search

An increasing number of studies support the hypothesis that smaller populations face a higher risk of extinction, and declining\\u000a population sizes are therefore one of the focal points in plant conservation. In small populations, loss of genetic diversity\\u000a is often related to reduced reproductive fitness. For the rare Dictamnus albus in Central Germany, an earlier study had already confirmed a

Isabell Hensen; Karsten Wesche

2006-01-01

33

Genetic Diversity and Human Equality.  

ERIC Educational Resources Information Center

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,…

Dobzhansky, Theodosius

34

Roles of lineage sorting and phylogenetic relationship in the genetic diversity at the self-incompatibility locus of Solanaceae.  

PubMed

Allelic polymorphism at the S locus that determines the gametophytic self-incompatibility (GSI) system in the pistil predates speciation. Understanding the evolution of a GSI system therefore requires knowledge of how lineage sorting and interspecific phylogenetic relationship affect S allele polymorphism. In searching for patterns of lineage sorting among species of various phylogenetic relationships, 22 S-alleles from 34 genets randomly taken at three Tennessee sites from a newly known GSI species Physalis longifolia were sequenced. Analyses of these data along with the previous sequences of three solanaceous species indicate that much of the combined allelic genealogy may be explained by lineage sorting and phylogenetic relationship. Using the mean terminal branch lengths of trans-specific alleles on the allelic genealogy to infer phylogenetic relationship among species, P. longifolia was found to be more closely related to P. cinerascens than to P. crassifolia. Nonetheless, the distribution of terminal branch lengths of P. longifolia was more similar to that of P. crassifolia than to that of P. cinerascens, suggesting phylogenetic relationship may have little effect on species-specific polymorphism. Similar habitat and growth characters, yet contrasting S-polymorphism, between P. longifolia and P. cinerascens also reject previous hypotheses that habitat and growth characters are the major factors responsible for interspecific differences in S-polymorphism. A likely scenario is that species-specific S-polymorphism is based on lineage sorting whose effect is further modified by species age and historical changes in population parameters. PMID:11380665

Lu, Y

2001-02-01

35

Genetic diversity of parasitic dinoflagellates in the genus amoebophrya and its relationship to parasite biology and biogeography.  

PubMed

We determined 18S rRNA gene sequences of Amoebophrya strains infecting the thecate dinoflagellates Alexandrium affine and Gonyaulax polygramma from Korean coastal waters and compared those data with previously reported sequences of Amoebophrya from cultures, infected cells concentrated from field samples, and environmental 18S rRNA gene sequences obtained from a variety of marine environments. Further, we used these data to examine genetic diversity in Amoebophrya strains relative to geographic origin, host phylogeny, site of infection, and host specificity. In our analyses of known dinoflagellate taxa, the 13 available Amoebophrya sequences clustered together within the dinoflagellates as three groups forming a monophyletic group with high bootstrap support (maximum likelihood, ML: 100%) or a posterior probability (PP) of 1. When the Amoebophrya sequences were analyzed along with environmental sequences associated with Marine Alveolate Group II, nine subgroups formed a monophyletic group with high bootstrap support (ML: 100%) and PP of 1. Sequences known to be from Amoebophrya spp. infecting dinoflagellate hosts were distributed in seven of those subgroups. Despite differences in host species and geographic origin (Korea, United States, and Europe), Amoebophrya strains (Group II) from Gymnodinium instriatum, A. affine, Ceratium tripos (AY208892), Prorocentrum micans, and Ceratium lineatum grouped together by all of our tree construction methods, even after adding the environmental sequences. By contrast, strains within Groups I and III divided into several lineages following inclusion of environmental sequences. While Amoebophrya strains within Group II mostly developed within the host cytoplasm, strains in Groups I and III formed infections inside the host nucleus, a trait that appeared across several of the subgroups. Host specificity varied from moderately to extremely species-specific within groups, including Group II. Taken together, our results imply that genetic diversity in Amoebophrya strains does not always reflect parasite biology or biogeography. PMID:18251796

Kim, Sunju; Park, Myung Gil; Kim, Keun-Yong; Kim, Chang-Hoon; Yih, Wonho; Park, Jong Soo; Coats, D Wayne

2008-01-01

36

Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers.  

PubMed

DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes. PMID:24783778

Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A

2014-01-01

37

Genetic selection and conservation of genetic diversity*.  

PubMed

For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. PMID:22827378

Blackburn, H D

2012-08-01

38

Rarity and genetic diversity in Indo-Pacific Acropora corals  

PubMed Central

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

Richards, Zoe T; Oppen, Madeleine J H

2012-01-01

39

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

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

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

2014-01-01

40

Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic  

PubMed Central

Background and Aims A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Methods Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. Key Results The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Conclusions Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north–south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera. PMID:19251716

Devey, Dion S.; Bateman, Richard M.; Fay, Michael F.; Hawkins, Julie A.

2009-01-01

41

ISSR analysis of genetic diversity in sacred lotus cultivars  

Microsoft Academic Search

In this study, inter-simple sequence repeats (ISSR) markers were applied to assess genetic diversity and genetic relationships of 92 cultivars of sacred lotus (Nelumbo nucifera Gaertn.), one of the most famous flowers in China. Our results showed that sacred lotus exhibited a low level of genetic diversity (percentage of polymorphic bands, PPB=55.8%), which may result from its asexual mode of

Yunyun Chen; Renchao Zhou; Xiaodong Lin; Keqiang Wu; Xuen Qian; Shangzhi Huang

2008-01-01

42

Genetic diversity of porcine sapoviruses.  

PubMed

Sapoviruses (SaVs) within the Caliciviridae family are an important cause of gastroenteritis in both humans and animals. Although the widespread occurrence of divergent human SaV strains has been reported, there have only been a few studies of porcine SaVs examining their genetic diversity. The aim of this study was to assess the genetic diversity of porcine SaVs in piglets with diarrhea in South Korea. Two hundred and thirty-seven fecal specimens from piglets with diarrhea were examined from 78 farms over a 2-year period from six provinces in South Korea. Overall, 69 (29.1%) of the samples from five provinces tested positive for porcine SaVs by either RT-PCR or nested PCR with the primer pairs specific to porcine SaVs. An analysis of the partial capsid gene (757bp) of 12 porcine SaVs detected from fecal samples showed genetic divergence, not only among the Korean porcine SaVs (67.7-99.1%), but also between Korean and American porcine SaVs (69.1-90.2%). Interestingly, one strain (Po/SaV/JN-MA113/05/Korea), formed a second porcine SaV/GIII genotype, and is tentatively called GIII/2. This strain had a 0.236-0.405 inter-cluster distance with the other strains in the same genogroup, which is comparable to the distances between the established GI and GII SaVs. Furthermore, two potential recombinant porcine SaVs were identified. In conclusion, porcine SaV infections are common in diarrheic piglets in South Korea. The infecting strains are genetically diverse, and include a newly recognized genotype and recombinant viruses within genogroup III. PMID:17382492

Jeong, Cheol; Park, Sang-Ik; Park, Sung-Hee; Kim, Ha-Hyun; Park, Su-Jin; Jeong, Jae-Ho; Choy, Hyon E; Saif, Linda J; Kim, Sang-Ki; Kang, Mun-Il; Hyun, Bang-Hun; Cho, Kyoung-Oh

2007-06-21

43

Relationships among Bacterial Cell Size, Productivity, and Genetic Diversity in Aquatic Environments using Cell Sorting and Flow Cytometry  

Microsoft Academic Search

The study of relationships between cell size and productivity is of key importance in microbial ecology to understand which\\u000a members of natural aquatic communities are responsible for the overall activity and\\/or productivity. Flow sorting of microorganisms\\u000a from different environmental samples was used to analyze the activity of bacterial cells depending on their biovolume. Bacterial\\u000a cells from five different natural samples

L. Bernard; C. Courties; P. Servais; M. Troussellier; M. Petit; P. Lebaron

2000-01-01

44

Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard ( Brassica juncea ) and its relationship to heterosis  

Microsoft Academic Search

RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism

A. Jain; S. Bhatia; S. S. Banga; S. Prakash; M. Lakshmikumaran

1994-01-01

45

High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution  

Microsoft Academic Search

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3«-untranslated region (3«-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis-Dioscorea

M. Bousalem; E. J. P. Douzery; D. Fargette

46

Genetic diversity-fitness correlation revealed by microsatellite analyses in European alpine marmots (Marmota marmota)  

Microsoft Academic Search

The relationship between individual genetic diversity and fitness-related traits are poorly understood in the wild. The availability of highly polymorphic molecular markers, such as microsatellites, has made research on this subject more feasible. We used three microsatellite-based measures of genetic diversity, individual heterozygosity H, mean d2 and mean d2outbreeding to test for a relationship between individual genetic diversity and important

A. Da Silva; G. Luikart; N. G. Yoccoz; A. Cohas; D. Allaine

2005-01-01

47

Genetic diversity, parasite prevalence and immunity in wild bumblebees.  

PubMed

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

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

2011-04-22

48

Evolution and genetic diversity of Theileria.  

PubMed

Theileria parasites infect a wide range of domestic and wild ruminants worldwide, causing diseases with varying degrees of severity. A broad classification, based on the parasite's ability to transform the leukocytes of host animals, divides Theileria into two groups, consisting of transforming and non-transforming species. The evolution of transforming Theileria has been accompanied by drastic changes in its genetic makeup, such as acquisition or expansion of gene families, which are thought to play critical roles in the transformation of host cells. Genetic variation among Theileria parasites is sometimes linked with host specificity and virulence in the parasites. Immunity against Theileria parasites primarily involves cell-mediated immune responses in the host. Immunodominance and major histocompatibility complex class I phenotype-specificity result in a host immunity that is tightly focused and strain-specific. Immune escape in Theileria is facilitated by genetic diversity in its antigenic determinants, which potentially results in a loss of T cell receptor recognition in its host. In the recent past, several reviews have focused on genetic diversity in the transforming species, Theileriaparva and Theileriaannulata. In contrast, genetic diversity in Theileriaorientalis, a benign non-transforming parasite, which occasionally causes disease outbreaks in cattle, has not been extensively examined. In this review, therefore, we provide an outline of the evolution of Theileria, which includes T. orientalis, and discuss the possible mechanisms generating genetic diversity among parasite populations. Additionally, we discuss the potential implications of a genetically diverse parasite population in the context of Theileria vaccine development. PMID:25102031

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

2014-10-01

49

Genetic and Metabolite Diversity of Sardinian Populations of Helichrysum italicum  

PubMed Central

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

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

2013-01-01

50

Network analyses structure genetic diversity in independent genetic worlds  

PubMed Central

DNA flows between chromosomes and mobile elements, following rules that are poorly understood. This limited knowledge is partly explained by the limits of current approaches to study the structure and evolution of genetic diversity. Network analyses of 119,381 homologous DNA families, sampled from 111 cellular genomes and from 165,529 phage, plasmid, and environmental virome sequences, offer challenging insights. Our results support a disconnected yet highly structured network of genetic diversity, revealing the existence of multiple “genetic worlds.” These divides define multiple isolated groups of DNA vehicles drawing on distinct gene pools. Mathematical studies of the centralities of these worlds’ subnetworks demonstrate that plasmids, not viruses, were key vectors of genetic exchange between bacterial chromosomes, both recently and in the past. Furthermore, network methodology introduces new ways of quantifying current sampling of genetic diversity. PMID:20007769

Halary, Sebastien; Leigh, Jessica W.; Cheaib, Bachar; Lopez, Philippe; Bapteste, Eric

2009-01-01

51

[Genetic diversity of DNA microsatellite for Tibetan Yak].  

PubMed

To assess the genetic diversity and relationship of the Tibetan yak breeds. The genetic diversity and phylogenies of a total of 480 individual from 11 Tibetan yak groups were analyzed using PCR and multiplex gel electrophoresis of silver staining technology with eight pairs of microsatellite markers.The result showed that these markers were highly polymorphic loci with rich genetic diversity in the Tibetan yak populations.The average polymorphic information content (PIC) in 11 groups of yak were higher than 0.5. The highest HEL13 was 0.8496, and the lowest TGLA57 was 0.7349. Among them, the PICof Dingqing yak was minimum (0.7505), indicating that the group is relatively pure.Sangri Yak had the highest PIC value (0.7949) indicating greater genetic variationwithinthe groups. Among the 11 groups examined, the order of heterozygosity size wasSangri(0.8193)>Jiangda(0.8190)>Sangsang(0.8157)>Baqing(0.8150)>Kangbu(0.8123)> Jiali(0.8087)>Gongbujiangda(0.8054)>Sibu(0.8041)>Leiwuqi(0.8033)>Pali(0.8031)>Dingqing(0.7831). The groups from eastern Tibet had grater genetic diversity than those from Western Tibet, which indicate that Tibet may be one of the cradles of the yak.According to the genetic distance, the cluster relationship constructed with UPGMA and NJ methods showed that 11 yak groups in Tibet could be divided into three forms. In summary,Tibet yak has abundant genetic diversity and the selected microsatellite markers can be used to evaluategenetic diversity of Tibetan yak. PMID:23448930

Li, Duo; Chai, Zhi-Xin; Ji, Qiu-Mei; Zhang, Cheng-Fu; Xin, Jin-Wei; Zhong, Jin-Cheng

2013-02-01

52

Genetic diversity-fitness correlation revealed by microsatellite analysesin European alpine marmots ( Marmota marmota )  

Microsoft Academic Search

The relationship between individual genetic diversity and fitness-related traits are poorly understood in the wild. The availability\\u000a of highly polymorphic molecular markers, such as microsatellites, has made research on this subject more feasible. We used\\u000a three microsatellite-based measures of genetic diversity, individual heterozygosity H, mean d\\u000a 2 and mean d\\u000a 2\\u000a outbreeding to test for a relationship between individual genetic

A. Da Silva; G. Luikart; N. G. Yoccoz; A. Cohas; D. Allainé

2006-01-01

53

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

PubMed Central

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

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

2012-01-01

54

A Brief Overview of Population Diversity Measures in Genetic Programming  

E-print Network

A Brief Overview of Population Diversity Measures in Genetic Programming Nguyen Thi Hien1, Nguyen a diversity measurement and controls this quantitative metric to maintain genetically diverse populations in a population. In Genetic Programming (GP), population diversity has been long considered as an important

Fernandez, Thomas

55

Flooding Stress: Acclimations and Genetic Diversity  

Microsoft Academic Search

Flooding is an environmental stress for many natural and man-made ecosystems worldwide. Genetic diversity in the plant response to flooding includes alterations in architecture, metabolism, and elon- gation growth associated with a low O2 escape strategy and an anti- thetical quiescence scheme that allows endurance of prolonged sub- mergence. Flooding is frequently accompanied with a reduction of cellular O2 content

J. Bailey-Serres; L. A. C. J. Voesenek

2008-01-01

56

High HIV1 genetic diversity in Cuba  

Microsoft Academic Search

Background: HIV-1 subtype B is largely predominant in the Caribbean, although other subtypes have been recently identified in Cuba. Objectives: To examine HIV-1 genetic diversity in Cuba. Methods: The study enrolled 105 HIV-1-infected individuals, 93 of whom had acquired the infection in Cuba. DNA from peripheral blood mononuclear cells was used for polymerase chain reaction amplification and sequencing of pol

Mar?a Teresa Cuevas; Ignacio Ruibal; Mar?a Luisa Villahermosa; He Ctor D?az; Elena Delgado; Elena Va Zquez-de Parga; Luc? Ap Erez-a Lvarez; Madel?n Blanco De Armas; Laureano Cuevas; Leandro Medrano; Enrique Noa; Saladin Osmanov; Rafael Na Jera; Michael M. Thomson

2002-01-01

57

Inducing Diverse Decision Forests with Genetic Programming  

E-print Network

Inducing Diverse Decision Forests with Genetic Programming Jan Such´y and Jir´i Kubal´ik Department@labe.felk.cvut.cz Abstract. This paper presents an algorithm for induction of ensem- bles of decision trees, also referred to as decision forests. In order to achieve high expressiveness the trees induced are multivariate, with var

Fernandez, Thomas

58

Does Genetic Diversity Predict Health in Humans?  

PubMed Central

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

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

2009-01-01

59

Genetic relationships among the oral streptococci.  

PubMed Central

Genetic relationships and species limits among the oral streptococci were determined by an analysis of electrophoretically demonstrable variation in 16 metabolic enzymes. Fifty isolates represented 40 electrophoretic types, among which the mean genetic diversity per locus was 0.857. Mannitol-1-phosphate dehydrogenase was not detected in isolates of the sanguis species complex, and glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase were absent in species of the mutans complex. Clustering from a matrix of Gower's coefficient of genetic similarity placed the 40 electrophoretic types in 10 well-defined groups corresponding to the Streptococcus species S. mutans, S. sobrinus, S. cricetus, S. rattus, S. ferus, S. oralis (mitior), two distinct assemblages of S. sanguis strains, and two subdivisions of "S. milleri." The assignments of isolates to these groups were the same as those indicated by DNA hybridization experiments, and the coefficient of correlation between genetic distance estimated by multilocus enzyme electrophoresis and genetic similarity indexed by DNA hybridization was -0.897 (P less than 0.001) for 50 pairwise combinations of isolates. S. ferus, which is widely believed to be a member of the mutans complex, was shown to be phylogenetically closer to species of the sanguis complex. PMID:3667531

Gilmour, M N; Whittam, T S; Kilian, M; Selander, R K

1987-01-01

60

Genetic diversity vs geographic distribution of five congeneric caddisflies  

Microsoft Academic Search

We compared the genetic structure and diversity offive Cheumatopsyche (Trichoptera:Hydropsychidae) species from Upper Three\\u000a Runs Creek inSouth Carolina to analyze the relationship betweengenetic variability and potential gene flow (i.e.,geographic\\u000a distribution) in a group of loticmacroinvertebrates. Among these species is an endemicto the stream (Cheumatopsyche richardsoni),\\u000a asoutheastern U.S.A. endemic (C. edista), andthree widely distributed species (C. pasella,C. pettiti, and C. pinaca).

Gordon R. Plague; J Vaun McArthur

1997-01-01

61

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...

62

Determination of Mitochondrial Genetic Diversity in Mammals  

PubMed Central

Mitochondrial DNA (mtDNA) is one of the most popular population genetic markers. Its relevance as an indicator of population size and history has recently been questioned by several large-scale studies in animals reporting evidence for recurrent adaptive evolution, at least in invertebrates. Here we focus on mammals, a more restricted taxonomic group for which the issue of mtDNA near neutrality is crucial. By analyzing the distribution of mtDNA diversity across species and relating it to allozyme diversity, life-history traits, and taxonomy, we show that (i) mtDNA in mammals does not reject the nearly neutral model; (ii) mtDNA diversity, however, is unrelated to any of the 14 life-history and ecological variables that we analyzed, including body mass, geographic range, and The World Conservation Union (IUCN) categorization; (iii) mtDNA diversity is highly variable between mammalian orders and families; (iv) this taxonomic effect is most likely explained by variations of mutation rate between lineages. These results are indicative of a strong stochasticity of effective population size in mammalian species. They suggest that, even in the absence of selection, mtDNA genetic diversity is essentially unpredictable, knowing species biology, and probably uncorrelated to species abundance. PMID:18202378

Nabholz, Benoit; Mauffrey, Jean-Francois; Bazin, Eric; Galtier, Nicolas; Glemin, Sylvain

2008-01-01

63

Genetic diversity of Brucella abortus isolates as determined by amplified fragment length polymorphism (AFLP) analysis  

E-print Network

with the powerful Bionumerics software package to determine the genetic relationships between B. abortus field isolates, collected from infections in wild herds of elk and bison to achieve a better understanding of the molecular diversity and evolution of B. abortus...

Bliss, Katherine Ann

2013-02-22

64

Factors influencing levels of genetic diversity in woody plant species  

Microsoft Academic Search

The plant allozyme literature was reviewed to: (1) compare genetic diversity in long-lived woody species with species representing other life forms, and (2) to investigate whether the levels and distribution of genetic diversity in woody species are related to life history and ecological characteristics. Data from 322 woody taxa were used to measure genetic diversity within species, and within and

J. L. Hamrick; Mary Jo W. Godt; Susan L. Sherman-Broyles

1992-01-01

65

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

PubMed

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

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

2006-11-01

66

Genetic relationships among merluccius species  

PubMed

Genetic data from nine species of Merluccius (Euro-African species merluccius, capensis, paradoxus, polli, senegalensis; American species bilinearis, productus, hubbsi, australis) from 21 informative allozyme loci provided insights into the phylogenetic and biogeographical relationships within the genus. The highest values of polymorphic loci and mean heterozygosity occur in the four American species. These values are consistent with large population sizes during speciation (through vicariant processes), and continuing through to the present. Conversely, the lower values of Euro-African species are consistent with bottlenecks occurring during or subsequent to speciation. Euro-African and American species formed two distinct clades. In the former group, merluccius, capensis and senegalensis clustered together as the most derived species, with distinct relationships between polli and paradoxus from an earlier divergence. Similarly, productus, australis and hubbsi clustered closely as the most derived American species, clearly diverging from the more ancestral bilinearis. Analyses including comparative data previously published for M. gayi indicated a close pairing to hubbsi. The data support a north-west Atlantic origin of the genus with unsampled M. albidus of broad Caribbean distribution proposed as the most primitive extant species. PMID:10447706

Roldan; Garcia-Marin; Utter; Pla

1999-07-01

67

Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations.  

PubMed

Genetic diversity is recognized as an important population attribute for both conservation and evolutionary purposes; however, the functional relationships between the environment, genetic diversity, and fitness-related traits are poorly understood. We examined relationships between selected lake parameters and population genetic diversity measures in 46 walleye (Sander vitreus) populations across the province of Ontario, Canada, and then tested for relationships between six life history traits (in three categories: growth, reproductive investment, and mortality) that are closely related to fitness, and genetic diversity measures (heterozygosity, d2, and Wright's inbreeding coefficient). Positive relationships were observed between lake surface area, growing degree days, number of species, and hatchery supplementation versus genetic diversity. Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females. The relationship between FIS and male early growth rate was negative and significant (P < 0.01) and marginally nonsignificant for females (P = 0.06), consistent with inbreeding depression effects. Only one significant relationship was observed for d2: female early growth rate (P < 0.05). Stepwise regression models showed that surface area and heterozygosity had a significant effect on female early growth rate, while hatchery supplementation, surface area and heterozygosity had a significant effect on male early growth rate. The strong relationship between lake parameters, such as surface area, and hatchery supplementation, versus genetic diversity suggests inbreeding and outbreeding in some of the populations; however, the weak relationships between genetic diversity and life history traits indicate that inbreeding and outbreeding depression are not yet seriously impacting Ontario walleye populations. PMID:16448402

Cena, Christopher J; Morgan, George E; Malette, Michael D; Heath, Daniel D

2006-02-01

68

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

USGS Publications Warehouse

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

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

2012-01-01

69

The silent threat of low genetic diversity  

USGS Publications Warehouse

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.

Hunter, Margaret E.

2013-01-01

70

Genetic Diversity and Competitive Abilities of Dalea purpurea (Fabaceae) from Remnant and Restored Grasslands  

Microsoft Academic Search

Allozyme and randomly amplified polymorphic DNA (RAPD) analyses were used to characterize the genetic relationships of Dalea purpurea from remnant and restored Illinois tallgrass prairies and a large remnant tallgrass prairie in Kansas. The remnant Illinois populations were less genetically diverse than the restored Illinois populations and the Kansas population. These restored Illinois populations were established with at least two

Danny J. Gustafson; David J. Gibson; Daniel L. Nickrent

2002-01-01

71

Allozyme diversity and phylogenetic relationships among diploid annual bromes (Bromus, Poaceae)  

Microsoft Academic Search

Phylogenetic relationships and genetic differentiation among eleven diploid annual brome species were evaluated by cladistic and phenetic analysis of the allozyme diversity of eight enzymes detected by PAGE. All species lacked heterozygous allozyme pheno- types, indicating prevalent autogamy and self-fertilization. Bromus japonicus Thunb. and B. squarrosus L. had the same allozymes, supporting their close genetic affinity. The placement of B.

Tatjana Oj; Vello Jaaska

1998-01-01

72

High genetic diversity is not essential for successful introduction  

PubMed Central

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

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

73

Highly structured genetic diversity of the Mycobacterium tuberculosis population in  

E-print Network

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti S, Djibouti Ville, Djibouti Abstract Djibouti is an East African country with a high tuberculosis incidence with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using

Choisy, Marc

74

Restoration of coral populations in light of genetic diversity estimates  

NASA Astrophysics Data System (ADS)

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

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

2009-09-01

75

Islands as refugia of Trifolium repens genetic diversity  

Microsoft Academic Search

Island populations are often thought to be more susceptible to the loss of genetic diversity as a consequence of limited population\\u000a size and genetic drift, greater susceptibility to detrimental stochastic events and low levels of immigration. However the\\u000a geographic isolation of islands may create refuges for native crop species whose genetic diversity is threatened from the\\u000a genetic erosion occurring in

Serene Hargreaves; Nigel Maxted; Ryoko Hirano; Michael Abberton; Leif Skøt; Brian V. Ford-Lloyd

2010-01-01

76

ORIGINAL PAPER Genetic worth and diversity across 18 years  

E-print Network

of year and clone fluctuations in strobili production on genetic worth, as well as on genetic diversity variation, and year-by-clone interaction in strobili production, the orchard's genetic worth was somewhat among clones may have an impact of the genetic val

Paris-Sud XI, Université de

77

Genetic diversity of Pasteurella species isolated from European vespertilionid bats.  

PubMed

Pasteurella are an important cause of fatal infections in free-ranging bats, but the genetic diversity of bat-derived strains is unclear. In the current study, 81 Pasteurella strains associated with pneumonia, severe organ necroses and systemic infection in free-ranging European vespertilionid bats were characterized by biochemical and molecular typing methods. Genetic relationships and subspecies status of Pasteurella multocida strains were determined by comparative 16S rDNA and rpoB gene sequence analysis. In addition, 30 representatives of the bat-derived P. multocida strains were selected based on phenotypic and genotypic tests to be compared by pulsed-field gel electrophoresis using SmaI. Most (85%) of the Pasteurella strains obtained from free-ranging bats in this study represented P. multocida ssp. septica. P. multocida ssp. multocida and Pasteurella species B were also identified in a small number of isolates. PFGE analysis correlated well with the sequencing results and revealed a high genetic diversity among bat-derived strains of P. multocida ssp. septica. Strains sharing identical or closely related SmaI fragment patterns were cultured from bats of different species, geographic origins, and years of isolation. The presence of numerous different P. multocida strains allows the assumption that Pasteurella infections in vespertilionid bats are not solely based on intra- but also on inter-species transmission. And indeed, our results present evidence of P. multocida infections in bats following cat predation. PMID:21050683

Mühldorfer, Kristin; Schwarz, Stefan; Fickel, Jörns; Wibbelt, Gudrun; Speck, Stephanie

2011-04-21

78

The LGBT advantage: Examining the relationship among sexual orientation diversity, diversity strategy, and performance  

Microsoft Academic Search

The purpose of this study was to examine the relationships among sexual orientation diversity, diversity strategy, and organizational performance. Data were gathered from 780 senior-level athletic administrators in 239 organizations. Moderated regression analysis indicated that, while main effects were not observed, there was a significant sexual orientation diversity×proactive diversity strategy interaction. Organizations with high sexual orientation diversity and that followed

George B. Cunningham

2011-01-01

79

The effect and relative importance of neutral genetic diversity for predicting parasitism varies across parasite taxa.  

PubMed

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

Ruiz-López, María José; Monello, Ryan J; Gompper, Matthew E; Eggert, Lori S

2012-01-01

80

The genetic diversity of forest tree species in French Guiana  

Microsoft Academic Search

In the early 1990s, INRA initiated a research project to describe and study the evolution of genetic diversity in the Guianan tropical forest. CIRAD joined the project shortly after it began. The basic objective of this project is to establish a general knowledge of the level and distribution of genetic diversity in tropical forests and its future dynamics. It is

Antoine Kremer

81

Genetic diversity of a newly established population of golden eagles on the Channel Islands, California  

USGS Publications Warehouse

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.

Sonsthagen, Sarah A.; Coonan, Timothy J.; Latta, Brian C.; Sage, George K.; Talbot, Sandra L.

2012-01-01

82

Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant.  

PubMed

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

Gruber, Monica A M; Hoffmann, Benjamin D; Ritchie, Peter A; Lester, Philip J

2012-09-01

83

Genetic Diversity Enhances Restoration Success by Augmenting Ecosystem Services  

PubMed Central

Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light) along a water–depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds) with high genetic diversity and from restoration techniques that can maintain that genetic diversity. PMID:22761681

Reynolds, Laura K.; McGlathery, Karen J.; Waycott, Michelle

2012-01-01

84

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

PubMed

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

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

2011-11-01

85

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

PubMed

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

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

2008-01-01

86

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

PubMed

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

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

2014-12-01

87

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

PubMed Central

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

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

2013-01-01

88

Multiple paternity does not depend on male genetic diversity  

PubMed Central

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

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

2014-01-01

89

Genetic diversity of Broussonetia papyrifera populations in southwest China.  

PubMed

Broussonetia papyrifera is an important native tree species with high economic value in southwest China. Its resources are drastically reduced because of over-harvesting and habitat fragmentation. In this study, 17 natural populations of B. papyrifera were analyzed using inter-simple sequence repeat (ISSR) markers to assess the genetic diversity and population structure. In total, 100 bands were obtained from 16 ISSR primers. The B. papyrifera populations showed relatively high genetic diversity at the species level [percentage of polymorphic bands (PPB): 96%; Nei's genetic diversity (HE): 0.3074; Shannon's information index (I): 0.4617], while the genetic diversity at the population level was relatively low (PPB: 53.2%; HE: 0.1826; I: 0.2735). Relatively high level of genetic differentiation among populations (41%) was disclosed by analysis of molecular variance, which agrees with the Nei's genetic diversity statistics (40.59%) and Shannon's information measure (40.76%). Gene flow among populations (NM) was only 0.7318. A significant correlation was observed between genetic and geographic distance among the studied populations (r = 0.2948). We conjectured that the genetic diversity of B. papyrifera resulted from human disturbance, habitat fragmentation, small effective population size, and geographic barrier. Given the high genetic differentiation among populations, some utilization and conservation strategies were proposed. This study provides a reference for the sustainable use of the species in southwest China. PMID:25222255

Liao, S X; Deng, Z H; Cui, K; Cui, Y Z; Zhang, C H

2014-01-01

90

Microsatellite analysis of genetic diversity and population genetic structure of Aegilops tauschii Coss. in Northern Iran  

Microsoft Academic Search

Genetic diversity and population genetic structure of Aegilops tauschii in Northern Iran were studied based on nine microsatellite loci. A high level of genetic diversity was observed from the\\u000a accessions collected from six regions (provinces). These accessions include 79 samples of the two subspecies (tauschii and strangulata), the intermediate form (among morphologically distinguished subspecies) and ten accessions of Triticum aestivum.

Mohammad Reza Naghavi; Mariam Hajikram; Ali Reza Taleei; Mohammad Jafar Aghaei

2010-01-01

91

Reconsideration for conservation units of wild Primula sieboldii in Japan based on adaptive diversity and molecular genetic diversity.  

PubMed

Primula sieboldii E. Morren is a perennial clonal herb that is widely distributed in Japan, but in danger of extinction in the wild. In a previous study, we revealed the genetic diversity of the species using chloroplast and nuclear DNA and used this information to define conservation units. However, we lacked information on adaptive genetic diversity, which is important for long-term survival and, thus, for the definition of conservation units. In order to identify adaptive traits that showed adaptive differentiation among populations, we studied the genetic variation in six quantitative traits within and among populations for 3 years in a common garden using 110 genets from five natural populations from three regions of Japan. The number of days to bud initiation was adaptive quantitative trait for which the degree of genetic differentiation among populations (QST) was considerably larger than that in eight microsatellite markers (FST). The relationship between this trait and environmental factors revealed that the number of days to bud initiation was negatively correlated, with the mean temperature during the growing period at each habitat. This suggests that adaptive differentiation in the delay before bud initiation was caused by selective pressure resulting from temperature differences among habitats. Our results suggest that based on adaptive diversity and neutral genetic diversity, the Saitama population represents a new conservation unit. PMID:19640318

Yoshida, Yasuko; Honjo, Masanori; Kitamoto, Naoko; Ohsawa, Ryo

2009-08-01

92

Flooding stress: acclimations and genetic diversity.  

PubMed

Flooding is an environmental stress for many natural and man-made ecosystems worldwide. Genetic diversity in the plant response to flooding includes alterations in architecture, metabolism, and elongation growth associated with a low O(2) escape strategy and an antithetical quiescence scheme that allows endurance of prolonged submergence. Flooding is frequently accompanied with a reduction of cellular O(2) content that is particularly severe when photosynthesis is limited or absent. This necessitates the production of ATP and regeneration of NAD(+) through anaerobic respiration. The examination of gene regulation and function in model systems provides insight into low-O(2)-sensing mechanisms and metabolic adjustments associated with controlled use of carbohydrate and ATP. At the developmental level, plants can escape the low-O(2) stress caused by flooding through multifaceted alterations in cellular and organ structure that promote access to and diffusion of O(2). These processes are driven by phytohormones, including ethylene, gibberellin, and abscisic acid. This exploration of natural variation in strategies that improve O(2) and carbohydrate status during flooding provides valuable resources for the improvement of crop endurance of an environmental adversity that is enhanced by global warming. PMID:18444902

Bailey-Serres, J; Voesenek, L A C J

2008-01-01

93

Genetic diversity of Echinococcus spp. in Russia.  

PubMed

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

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

94

Genetic diversity in Monilinia laxa populations in stone fruit species in Hungary.  

PubMed

The objectives of this study were firstly, to determine the genetic diversity of Monilinia laxa isolates from Hungary, using the PCR-based inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) technique; secondly, to prepare genetic diversity groups based on the dendrograms; and finally, to select some relevant isolates to study their fungicide sensitivity. 55 and 77 random amplified polymorphic ISSR and RAPD markers, of which 23 and 18 were polymorphic and 32 and 59 monomorphic, respectively, were used to assess the genetic diversity and to study the structure of M. laxa populations in Hungary. 27 isolates out of 57 ones were confirmed as M. laxa from several orchards (subpopulations) in three geographical regions, in various inoculum sources and in various hosts, were used. 10 fungicides and 12 isolates selected from genetic diversity groups based on the ISSR dendrograms were used to determine the fungicide sensitivity of the selected isolates. The analysis of population structure revealed that genetic diversity within locations, inoculum sources and host (H(S)) accounted for 99 % of the total genetic diversity (H(T)), while genetic diversity among locations, inoculum sources and host represented only 1 %. The relative magnitude of gene differentiation between subpopulations (G(ST)) and the estimate of the number of migrants per generation (Nm) averaged 0.005-0.009 and 53.9-99.2, respectively, for both ISSR and RAPD data set. The results obtained in dendrograms were in accordance with the gene diversity analysis. Grouping of isolates in the dendrograms was irrespective of whether they came from the same or different geographical locations. There was no relationship between clustering among isolates from inoculum sources and hosts. In the fungicide sensitivity tests, five isolates out of 12 were partly insensitive to boscalid+piraclostrobin, cyprodinil, fenhexamid or prochloraz. Obtained results in genetic diversity of M. laxa populations are discussed together with implications for the management of brown rot. PMID:24474390

Fazekas, Mónika; Madar, Anett; Sipiczki, Matthias; Miklós, Ida; Holb, Imre J

2014-06-01

95

Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR.  

PubMed

Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe. PMID:24533164

Teixeira, Helena; Rodríguez-Echeverría, Susana; Nabais, Cristina

2014-01-01

96

Genetic Diversity and Differentiation of Juniperus thurifera in Spain and Morocco as Determined by SSR  

PubMed Central

Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe. PMID:24533164

Teixeira, Helena; Rodriguez-Echeverria, Susana; Nabais, Cristina

2014-01-01

97

Genetic diversity and its consequences for light adaptation in Prochlorococcus  

E-print Network

When different cells thrive across diverse environments, their genetic differences can reveal what genes are essential to survival in a particular environment. Prochlorococcus, a cyanobacterium that dominates the open ...

Kettler, Gregory C. (Gregory Carl)

2011-01-01

98

GENETIC DIVERSITY AND STRAIN IMPROVEMENT IN Pleurotus ostreatus;.  

E-print Network

??newline Department of Plant Pathology newlineCSK Himachal Pradesh Krishi Vishvavidyalaya newlinePalampur-176062 newline newlineTitle of the thesis : Genetic diversity and Strain Improvement in Pleurotus ostreatus.… (more)

Sharma, Rishu

2007-01-01

99

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

PubMed

Studying the genetic diversity of wild populations that are affected by pollution provides a basis for estimating the risks of environmental contamination to both wildlife, and indirectly to humans. Such research strives to produce both a better understanding of the underlying mechanisms by which genetic diversity is affected,and the long-term effects of the pollutants involved.In this review, we summarize key aspects of the field of genetic ecotoxicology that encompasses using genetic patterns to examine metal pollutants as environmental stressors of natural animal populations. We address genetic changes that result from xenobiotic exposure versus genetic alterations that result from natural ecological processes. We also describe the relationship between metal exposure and changes in the genetic diversity of chronically exposed populations, and how the affected populations respond to environmental stress. Further, we assess the genetic diversity of animal populations that were exposed to metals, focusing on the literature that has been published since the year 2000.Our review disclosed that the most common metals found in aquatic and terrestrial ecosystems were Cd, Zn, Cu and Pb; however, differences in the occurrence between aquatic (Cd=Zn>Cu>Pb>Hg) and terrestrial (Cu>Cd>Pb>Zn>Ni)environments were observed. Several molecular markers were used to assess genetic diversity in impacted populations, the order of the most common ones of which were SSR's > allozyme > RAPD's > mtDNA sequencing> other molecular markers.Genetic diversity was reduced for nearly all animal populations that were exposed to a single metal, or a mixture of metals in aquatic ecosystems (except in Hyalella azteca, Littorina littorea, Salmo trutta, and Gobio gobio); however, the pattern was less clear when terrestrial ecosystems were analyzed.We propose that future research in the topic area of this paper emphasizes seven key areas of activity that pertain to the methodological design of genetic ecotoxicological studies. Collectively, these points are designed to provide more accurate data and a deeper understanding of the relationship between alterations in genetic diversity of impacted populations and metal exposures. In particular, we believe that the exact nature of all tested chemical pollutants be clearly described, biomarkers be included, sentinel organisms be used, testing be performed at multiple experimental sites, reference populations be sampled in close geographical proximity to where pollution occurs, and genetic structure parameters and high-throughput technology be more actively employed. Furthermore, we propose a new class of biomarkers,termed "biomarkers of permanent effect," which may include measures of genetic variability in impacted populations. PMID:24158580

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

2014-01-01

100

Genetic Resources and the Convention on Biological Diversity  

NSDL National Science Digital Library

This peer-reviewed article from BioScience is about effect the convention on biological diversity had on US genetic resources. At a meeting in Brazil in March, the Convention on Biological Diversity moved a step closer to finalizing an international regulatory regime for access to and benefit sharing of genetic resources. Discussions now under way will be influential in determining policies governing biodiversity research and bioprospecting.

RICHARD BLAUSTEIN (;)

2006-07-01

101

LOW GENETIC DIVERSITY IN THE ANTARCTIC TOOTHFISH (DISSOSTICHUS MAWSONI) OBSERVED WITH MITOCHONDRIAL AND INTRON DNA MARKERS  

Microsoft Academic Search

Two molecular methods, mitochondrial and intron DNA markers, were used to determine genetic relationships among Antarctic toothfi sh (Dissostichus mawsoni) samples from three CCAMLR areas: Subareas 48.1 and 88.1 and Division 58.4.2. D. mawsoni appeared to be characterised by low diversity; no genetic variation was detected with restriction enzyme digests of nine sub-regions of the mitochondrial genome. Polymorphisms were found

P. J. Smith

2005-01-01

102

Genetic Diversity of Bacillus cereus \\/ B. thuringiensis Isolates from Natural Sources  

Microsoft Academic Search

.   The genetic diversity and relationships among 154 Bacillus cereus\\/B. thuringiensis isolates recovered from soil samples from five geographic areas in Norway were investigated with multilocus enzyme electrophoresis\\u000a (MEE). Cluster analysis revealed two major groups (designated cluster I and cluster II) separated at genetic distance greater\\u000a than 0.55. Cluster I included 62 electrophoretic types (ETs) originating from all five locations,

Erlendur Helgason; Dominique A. Caugant; Marguerite-M. Lecadet; Yahua Chen; Jacques Mahillon; Ann Lövgren; Ida Hegna; Kirsti Kvaløy; Anne-Brit Kolstø

1998-01-01

103

Comparative analysis of genetic diversity in sacred lotus ( Nelumbo nucifera Gaertn.) using AFLP and SSR markers  

Microsoft Academic Search

The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred\\u000a lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions\\u000a of N.\\u000a nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7

Jihong HuLei; Lei Pan; Honggao Liu; Shuzhen Wang; Zhihua Wu; Weidong Ke; Yi Ding

104

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

PubMed

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

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

2014-01-01

105

Genetic diversity in Ethiopian barley in relation to altitude  

Microsoft Academic Search

A representative sample of the Ethiopian barley collection, maintained at the Ethiopian Plant Genetic Resources Centre (PGRC\\/E), was studied for its phenotypic diversity for some agronomic characters, i.e. kernel row number, spike density, spikelets per spike, caryopsis type, kernel colour, thousand grain weight, days to maturity and plant height. The diversity was estimated by using the Shannon-Weaver diversity index (H')

J. M. M. Engels

1994-01-01

106

Genetic diversity among watermelon (Citrullus lanatus and Citrullus colocynthis) accessions  

Microsoft Academic Search

Genetic diversity was estimated among 42 U.S. Plant Introduction (PI) accessions of the genus Citrullus (of these, 34 PIs are reported to have disease resistance), and 5 watermelon cultivars, using 30 RAPD primers. These primers produced 662 RAPD markers that could be rated with high confidence. Based on these markers, genetic similarity coefficients were calculated and a dendrogram was constructed

Amnon Levi; Claude E. Thomas; Anthony P. Keinath; Todd C. Wehner

2001-01-01

107

Historical origins and genetic diversity of wine grapes  

Microsoft Academic Search

Thegenomicresourcesthatareavailabletothegrapevine research community have increased enormously during the past five years, in parallel with a renewed interest in grapevine (Vitis vinifera L.) germplasm resources and analysis of genetic diversity in grapes. Genetic variation, either natural or induced, is invaluable for crop improvement and understanding gene function, and the same is true for the grapevine. The history and vineyard cultural practices

Patrice This; Thierry Lacombe; Mark R. Thomas

2006-01-01

108

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

PubMed Central

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

Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge

2013-01-01

109

The Genetic Relationship between Indentical Twins.  

ERIC Educational Resources Information Center

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…

Herman, Rosemary

1984-01-01

110

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

USGS Publications Warehouse

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.

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

2009-01-01

111

COMPARING LINGUISTIC AND GENETIC RELATIONSHIPS AMONG EAST ASIAN POPULATIONS: A STUDY OF THE RH  

E-print Network

396 CHAPTER 15 COMPARING LINGUISTIC AND GENETIC RELATIONSHIPS AMONG EAST ASIAN POPULATIONS: A STUDY regions settled by our species, Homo sapiens sapiens, after Africa and the Middle East (Lahr and Foley of our species. Moreover, documenting the genetic diversity of East Asian populations is a crucial step

Paris-Sud XI, Université de

112

Plant Chitinases: Genetic Diversity and Physiological Roles  

Microsoft Academic Search

Chitinase proteins are widely distributed across diverse biological systems. Chitinases hydrolyze chitin, chitosan, lipochitooligosaccharides, peptidoglycan, arabinogalactan and glycoproteins containing N-acetylglucosamine. Analyses of genome-wide sequence and microarray expression profilings show that chitinase genes are represented by large families and the individual member genes are expressed in diverse conditions. Chitinase proteins are members in the group of the pathogenesis-related proteins that are

Anita Grover

2012-01-01

113

Limited Genetic Diversity in the Endophytic Sugarcane Bacterium Acetobacter diazotrophicus  

PubMed Central

Acetobacter diazotrophicus isolates that originated from different sugarcane cultivars growing in diverse geographic regions of Mexico and Brazil were shown to have limited genetic diversity. Measurements of polymorphism in the electrophoretic mobilities of metabolic enzymes revealed that the mean genetic diversity per enzyme locus (among the four electrophoretic types distinguished) was 0.064. The results of the genetic analysis indicate that the genetic structure of A. diazotrophicus is clonal, with one largely predominant clone. Plasmids were present in 20 of 24 isolates, and the molecular sizes of the plasmids ranged from 2.0 to 170 kb. Two plasmids (a 20- to 24-kb plasmid detected in all 20 plasmid-containing isolates and a 170-kb plasmid observed in 14 isolates) were highly conserved among the isolates examined. Regardless of the presence of plasmids, all of the isolates shared a common pattern of nif structural gene organization on the chromosome. Images PMID:16349254

Caballero-Mellado, Jesus; Martinez-Romero, Esperanza

1994-01-01

114

Rates of inbreeding and genetic diversity in Iranian Holstein Cattle.  

PubMed

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1?048?572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non-founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non-founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co-ancestry and inbreeding, which would lead to better handling of the effective population size. PMID:25041055

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

2014-10-01

115

High genetic diversity in a remote island population system: sans Eric F. Karlin1  

E-print Network

words: allopolyploid, bryophyte, clone, genetic diversity, Hawaii, long-distance dispersal, SphagnumHigh genetic diversity in a remote island population system: sans sex Eric F. Karlin1 , Sara C genetic diversity to that found in populations of S. palustre in other regions. · The genetic diversity

Wisconsin at Madison, University of

116

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

PubMed

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

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

2013-11-01

117

Symbiotic and Genetic Diversity of Rhizobium galegae Isolates Collected from the Galega orientalis Gene Center in the Caucasus  

Microsoft Academic Search

This paper explores the relationship between the genetic diversity of rhizobia and the morphological diversity of their plant hosts. Rhizobium galegae strains were isolated from nodules of wild Galega orientalis and Galega officinalis in the Caucasus, the center of origin for G. orientalis. All 101 isolates were characterized by genomic amplified fragment length polymorphism fingerprinting and by PCR-restriction fragment length

E. E. Andronov; Z. Terefework; M. L. Roumiantseva; N. I. Dzyubenko; O. P. Onichtchouk; O. N. Kurchak; A. Dresler-Nurmi; J. P. W. Young; B. V. Simarov; K. Lindstrom

2003-01-01

118

Low Genetic Differentiation of and Close Evolutionary Relationships between Anas platyrhynchos and Anas poecilorhyncha : RAPD–PCR Evidence  

Microsoft Academic Search

Using RAPD–PCR, we examined genetic diversity and phylogenetic relationships in two groups of river ducks: Anas platyrhynchos, A. poecilorhyncha, A. streperaand A. crecca, A. formosa, A. querquedula. Molecular taxon-specific markers were found for teals (A. crecca, A. formosa, A. querquedula) and gadwall (A. strepera). Each of the species examined was shown to exhibit high genetic diversity. The mean levels of

I. V. Kulikova; G. N. Chelomina; Yu. N. Zhuravlev

2003-01-01

119

Clonal structure and genetic diversity of three desert phreatophytes.  

PubMed

The objective of this paper was to assess clone sizes of three perennial desert plant species with AFLP markers and to relate them to clonal and genetic diversity and to hydroecology. The study was carried out at the southern rim of the Taklamakan Desert, where sexual regeneration is only possible shortly after rare flooding events, resulting in rarely established cohorts with subsequent extensive vertical growth and horizontal clonal spread. In this environment, repeated seedling establishment is excluded. We expected decreasing clonal and genetic diversity with increasing clone size and increasing distance to the groundwater table and a common response pattern among all study species. Maximum sizes of Populus euphratica and Alhagi sparsifolia clones were 121 ha and 6.1 ha, respectively, while Tamarix ramosissima clones reached a maximum size of only 38 m(2). In P. euphratica and A. sparsifolia, clonal diversity declined with increasing clone size and increasing distance to the groundwater table, while genetic diversity remained unaffected. Tamarix ramosissima differed from the other species because of a much smaller clonality. Clone size and clonal diversity were found to be good proxy variables for clone age. Despite the considerable age of the clones, genetic diversity is maintained in the populations. PMID:21622383

Vonlanthen, Beatrix; Zhang, Ximing; Bruelheide, Helge

2010-02-01

120

Genetic diversity of pigeon circovirus in Hungary.  

PubMed

Pigeon circoviruses (PiCV) had been identified worldwide and are responsible for immune suppression and a variety of diseases collectively referred to as young pigeon disease syndrome. Samples from racing pigeons were collected throughout Hungary and analyzed for the presence of PiCV by polymerase chain reaction. The capsid protein coding gene was amplified from ten PiCVs of different origins, and compared with known PiCV sequences. The results indicated that PiCV was highly variable, the viruses formed five distinct genetic groups. Differences of the 3' end of the gene suggested the possibility of genetic recombination among these groups. PMID:21922293

Cságola, Attila; Lorincz, Márta; Tombácz, Kata; Wladár, Zsófia; Kovács, Eszter; Tuboly, Tamás

2012-02-01

121

Endophytic fungi alter relationships between diversity and ecosystem properties  

Microsoft Academic Search

Recent studies have expanded research on biodiversity by investigating whether the effects of diversity on ecosystem functioning hinge on the presence of symbiotic microorganisms. Cool-season grasses commonly harbour endophytic fungi that can enhance plant resistance to herbivory, drought and competition. We address whether these endosymbionts modify relationships between diversity and two ecosystem properties: productivity and invasibility. We develop a graphical

Jennifer A. Rudgers; Jennifer M. Koslow; Keith Clay

2004-01-01

122

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

PubMed Central

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 (60·7 % L-morph). On the other hand, no significant difference in pairwise genetic distances between populations was observed between L- (0·107) and S-morphs (0·106). 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

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

2012-01-01

123

Genetic Diversity and Genetic Differentiation in Daphnia Metapopulations With Subpopulations of Known Age  

PubMed Central

If colonization of empty habitat patches causes genetic bottlenecks, freshly founded, young populations should be genetically less diverse than older ones that may have experienced successive rounds of immigration. This can be studied in metapopulations with subpopulations of known age. We studied allozyme variation in metapopulations of two species of water fleas (Daphnia) in the skerry archipelago of southern Finland. These populations have been monitored since 1982. Screening 49 populations of D. longispina and 77 populations of D. magna, separated by distances of 1.5–2180 m, we found that local genetic diversity increased with population age whereas pairwise differentiation among pools decreased with population age. These patterns persisted even after controlling for several potentially confounding ecological variables, indicating that extinction and recolonization dynamics decrease local genetic diversity and increase genetic differentiation in these metapopulations by causing genetic bottlenecks during colonization. We suggest that the effect of these bottlenecks may be twofold, namely decreasing genetic diversity by random sampling and leading to population-wide inbreeding. Subsequent immigration then may not only introduce new genetic material, but also lead to the production of noninbred hybrids, selection for which may cause immigrant alleles to increase in frequency, thus leading to increased genetic diversity in older populations. PMID:15937138

Haag, Christoph R.; Riek, Myriam; Hottinger, Jurgen W.; Pajunen, V. Ilmari; Ebert, Dieter

2005-01-01

124

The study of relatedness and genetic diversity in cranes  

USGS Publications Warehouse

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.

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

1992-01-01

125

A new genetic operator maintaining population diversity  

NASA Astrophysics Data System (ADS)

The paper describes an enhancement of the traditional 2-point crossover operator used for binary representation in genetic algorithms. This operator preserves a schema common to both parent chromosomes. The enhancement of its functionality is in a modified treatment of this common schema. The offspring produced by the modified operator is partially randomized so that it contains both the common schema and its binary complement. It helps to prevent the genetic algorithms from getting stuck in a local optimum and enhance the exploration of the search space beyond the limits imposed by the classical operator's functionality. The partially randomized 2-point crossover operator has been tested on a number of different problems and compared to the original 2-point operator.

Kubalík, Ji?í; Lažanský, Ji?í

2001-06-01

126

Genetic diversity of Actinobacillus lignieresii isolates from different hosts  

PubMed Central

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacilus lignieresii isolates from different hosts and geographic localities is described. On the basis of variances in AFLP profiles, the strains were grouped in two major clusters; one comprising strains isolated from horses and infected wounds of humans bitten by horses and another consisting of strains isolated from bovine and ovine hosts. The present data indicate a comparatively higher degree of genetic diversity among strains isolated from equine hosts and confirm the existence of a separate genomospecies for A. lignieresi-like isolates from horses. Among the isolates from bovine and ovine hosts some clonal lines appear to be genetically stable over time and could be detected at very distant geographic localities. Although all ovine strains investigated grouped in a single cluster, the existence of distinct genetic lineages that have evolved specificity for ovine hosts is not obvious and needs to be confirmed in other studies. PMID:21303512

2011-01-01

127

AFLP Analyses of Genetic Diversity in Bentgrass  

Microsoft Academic Search

ABSTRACT,Vasey are known to exist in tetraploid and hexaploid forms (2n 6x 42). In a wide collection of A. gigantea, Bentgrasses (Agrostis spp.) are widely occurring temperate grasses Jones (1955a) only found,hexaploids. Because of the with more than 220 species that represent a vast resource for genetic outcrossing nature of bentgrass, ploidy levels need to improvement of turfgrass cultivars. Bentgrasses

G. V. Vergara; S. S. Bughrara

2003-01-01

128

Genetic Diversity in the Interference Selection Limit  

PubMed Central

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

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

2014-01-01

129

Genetic diversity in the interference selection limit.  

PubMed

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

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

2014-03-01

130

Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis  

PubMed Central

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

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

2011-01-01

131

HIV1 Genetic Diversity in Antenatal Cohort, Canada  

Microsoft Academic Search

We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylo- genetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%)

Bertine S. Akouamba; Janique Viel; Hugues Charest; Natacha Merindol; Johanne Samson; Normand Lapointe; Bluma G. Brenner; Richard Lalonde; P. Richard Harrigan; Marc Boucher; Hugo Soudeyns

132

How frequency and intensity shape diversity–disturbance relationships  

PubMed Central

Understanding the relationship between disturbance regimes and species diversity has been of central interest to ecologists for decades. For example, the intermediate disturbance hypothesis proposes that diversity will be highest at intermediate levels of disturbance. Although peaked (hump-shaped) diversity–disturbance relationships (DDRs) have been documented in nature, many other DDRs have been reported as well. Here, we begin to theoretically unify these diverse empirical findings by showing how a single simple model can generate several different DDRs, depending on the aspect of disturbance that is considered. Additionally, we elucidate the competition-mediated mechanism underlying our results. Our findings have the potential to reconcile apparently conflicting empirical results on the effects of disturbance on diversity. PMID:21422284

Miller, Adam D.; Roxburgh, Stephen H.; Shea, Katriona

2011-01-01

133

Genetic diversity among ancient Nordic populations.  

PubMed

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

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

2010-01-01

134

High-Pitched Notes during Vocal Contests Signal Genetic Diversity in Ocellated Antbirds  

PubMed Central

Animals use honest signals to assess the quality of competitors during aggressive interactions. Current theory predicts that honest signals should be costly to produce and thus reveal some aspects of the phenotypic or genetic quality of the sender. In songbirds, research indicates that biomechanical constraints make the production of some acoustic features costly. Furthermore, recent studies have found that vocal features are related to genetic diversity. We linked these two lines of research by evaluating if constrained acoustic features reveal male genetic diversity during aggressive interactions in ocellated antbirds (Phaenostictus mcleannani). We recorded the aggressive vocalizations of radiotagged males at La Selva Biological Station in Costa Rica, and found significant variation in the highest frequency produced among individuals. Moreover, we detected a negative relationship between the frequency of the highest pitched note and vocalization duration, suggesting that high pitched notes might constrain the duration of vocalizations through biomechanical and/or energetic limitations. When we experimentally exposed wild radiotagged males to simulated acoustic challenges, the birds increased the pitch of their vocalization. We also found that individuals with higher genetic diversity (as measured by zygosity across 9 microsatellite loci) produced notes of higher pitch during aggressive interactions. Overall, our results suggest that the ability to produce high pitched notes is an honest indicator of male genetic diversity in male-male aggressive interactions. PMID:19956580

Araya-Ajoy, Yi-men; Chaves-Campos, Johel; Kalko, Elisabeth K. V.; DeWoody, J. Andrew

2009-01-01

135

Simple sequence repeat analysis of genetic diversity in primary core collection of peach (Prunus persica).  

PubMed

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach (Prunus persica (L.) Batsch) was evaluated by using simple sequence repeats (SSRs). The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach > Crisp peach > Flat peach > Nectarine > Honey Peach > Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging (UPGMA) placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach. PMID:18666957

Li, Tian-Hong; Li, Yin-Xia; Li, Zi-Chao; Zhang, Hong-Liang; Qi, Yong-Wen; Wang, Tao

2008-01-01

136

Analysis of genetic diversity through population history Nicholas Freitag McPhee and Nicholas J. Hopper  

E-print Network

Analysis of genetic diversity through population history Nicholas Freitag McPhee and Nicholas J of a population based on the genetic history of the individuals. We then apply these measures to the genetic of diversity in GP populations is indeed a significant issue. 1.1 MEASURING GENETIC DIVERSITY One

Minnesota, University of

137

Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L.  

PubMed

Phaseolus coccineus L. is closely related to P. vulgaris and is the third most important cultivated Phaseolus species. Little is known about the patterns of its diversity. In this work, a representative collection of its worldwide diversity was initially developed. The collection includes 28 wild forms (WFs) and 52 landraces (LRs) from Mesoamerica (the crop domestication area), and 148 LRs from Europe (where the crop was introduced in the sixteenth century). The collection was studied by using 12 SSR molecular markers that were developed for the P. vulgaris genome. They were proved to be effective and reliable in P. coccineus in this work. Fourteen LRs of P. dumosus (previously identified as a subspecies of P. coccineus) were also studied. The genetic diversity, population structure and phylogenetic relationships were investigated. The results indicate that: (a) the European and Mesoamerican gene pools are clearly differentiated, (b) a certain reduction of diversity occurred with introduction into Europe, and (c) the Mesoamerican LRs (P. dumosus included) and WFs are closely related and are connected by a high gene flow. Inferences on the domestication process of P. coccineus are also presented. This study provides a picture of the genetic diversity distribution and outcomes with introduction into the Old World, which was not available before. It also underlines that the genetic diversity of both WFs and LRs is an important source for Phaseolus spp. breeding programs and deserves to be preserved in situ and ex situ. PMID:21279322

Spataro, G; Tiranti, B; Arcaleni, P; Bellucci, E; Attene, G; Papa, R; Spagnoletti Zeuli, P; Negri, V

2011-05-01

138

[AFLP analysis on genetic diversity of wild Dactylis glomerata L. germplasm resources].  

PubMed

Thirty-seven accessions of wild Dactylis glomerata L. were used in assessment of genetic diversity by means of amplified fragment length polymorphism (AFLP). Nine primer pairs were selected from 64 preparations and then used to analyze the plant materials. A total of 400 DNA fragments were amplified, among which 336 (84.0%) were polymorphic. Genetic distance, from 0.0692-0.4214 among accessions, was calculated by the NTSYS-pc software. A dendrogram was constructed using UPGMA based on genetic distance matrix. Eight clusters were defined at the genetic similarity of 0.81. A two-dimensional PCO plot representing relationships among accessions was also produced by EIGEN, demonstrating the same distribution pattern as from the cluster analysis. Based on molecular analysis, the genetic variation of D. glomerata germplasms was closely associated with ploidy levels and geographical distributions. PMID:16825173

Peng, Yan; Zhang, Xin-Quan; Liu, Jin-Ping; Yi, Yang-Jie

2006-07-01

139

Analysis of genetic diversity in accessions of Irvingia gabonensis (Aubry-Lecomte ex O'Rorke) Baill  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) was used to assess genetic diversity and relationships among 15 accessions of Irvingia gabonensis collected from Cameroun, Gabon, and Nigeria. Twelve AFLP+3 primers produced 384 polymorphic fragments. Average genetic distance (AGD) between the 15 accessions was 58.7% (32-88%). AGD and range of genetic distance among accessions from Cameroun, Nigeria and Gabon were 62% (53-76%), 52%

G. N. Ude; C. O. Dimkpa; P. O. Anegbeh; A. A. Shaibu; A. Tenkouano; M. Pillay; Z. Tchoundjeu

140

Coalescence and genetic diversity in sexual populations under selection.  

PubMed

In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic "linkage block" with a characteristic length, , determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra compared with computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics. PMID:24019480

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

2013-09-24

141

Genetic diversity is overlooked in international conservation policy implementation  

E-print Network

worldwide are parts of the World Association of Zoos and Aquariums (www.waza.org) and similar regional. This realiza- tion has prompted agreements by world leaders to conserve genetic diversity. By this year, 2010, world leaders have agreed that a significant reduction of the rate of biodiversity loss

142

Is Trypanosoma vivax genetically diverse? Patrick B. Hamilton  

E-print Network

GAPDH gene sequences from across West Africa (The Gambia, Nigeria and Cameroon) and South America [8 the true genetic diversity of T. vivax in West Africa, particularly as T. vivax has not been extensively of Trypanosoma (Duttonella) vivax isolates from East Africa and West Africa. Int. J. Parasitol. 20, 389­394 4

Tyler, Charles

143

Genetic Diversity within Human Erythroviruses: Identification of Three Genotypes  

Microsoft Academic Search

B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of

Annabelle Servant; Syria Laperche; Francis Lallemand; Valerie Marinho; Guillemette De Saint Maur; Jean Francois Meritet; Antoine Garbarg-Chenon

2002-01-01

144

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

E-print Network

Genetic calibration of species diversity among North America's freshwater fishes Julien Aprila,1 by the Editorial Board May 7, 2011 (received for review November 4, 2010) Freshwater ecosystems are being heavily specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species

Bernatchez, Louis

145

Genetic diversity and management of Nearctic rock ptarmigan (Lagopus mutus)  

E-print Network

Genetic diversity and management of Nearctic rock ptarmigan (Lagopus mutus) Karen Holder, Robert Montgomerie, and Vicki L. Friesen Abstract: Though the rock ptarmigan, Lagopus mutus (Montin, 1776: Lagopus mutus evermanni (Elliot, 1896) on Attu I., Alaska, Lagopus mutus welchi (Brewster, 1885

Montgomerie, Bob

146

ORIGINAL PAPER Genetic diversity and structure of western white pine  

E-print Network

of white pine blister rust) and reduced opportunities for regeneration. Amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity and structure among populations at 15, regeneration ability, and occupancy of sites make WWP highly desirable throughout its range. Under optimal

147

Genetic Diversity of Argentine Isolates of Feline Immunodeficiency Virus  

Microsoft Academic Search

We report the nucleotide sequence and genetic diversity of part of the envelope (env) gene of four strains of feline immunodeficiency virus (FIV) isol- ated from Argentine domestic cats. The DNA enco- ding the V3 to V5 regions of the env gene of the FIV isolates were amplified by PCR, cloned and sequ- enced. Phylogenetic analysis revealed that the Argentine

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

1996-01-01

148

Coalescence and genetic diversity in sexual populations under selection  

PubMed Central

In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic “linkage block” with a characteristic length, , determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra compared with computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics. PMID:24019480

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

2013-01-01

149

ORIGINAL PAPER Genetic diversity affects colony survivorship in commercial  

E-print Network

drones), although there is much variation among queens. One main consequence of such extreme polyandry, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate is the single queen of a Communicated by: Sven Thatje D. R. Tarpy (*) Department of Entomology, North Carolina

Tarpy, David R.

150

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

PubMed Central

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 = 0·76) and a relatively low inbreeding coefficient (FIS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G?ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) 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 western–eastern differentiation in this species merits consideration in future conservation efforts. PMID:19797423

AEgisdottir, Hafdis Hanna; Kuss, Patrick; Stocklin, Jurg

2009-01-01

151

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

PubMed

We review previous studies on the genetic diversity of malaria vectors to highlight the major trends in population structure and demographic history. In doing so, we outline key information about molecular markers, sampling strategies and approaches to investigate the causes of genetic structure in Anopheles mosquitoes. Restricted gene flow due to isolation by distance and physical barriers to dispersal may explain the spatial pattern of current genetic diversity in some Anopheles species. Nonetheless, there is noteworthy disagreement among studies, perhaps due to variation in sampling methodologies, choice of molecular markers, and/or analytical approaches. More refined genealogical methods of population analysis allowing for the inclusion of the temporal component of genetic diversity facilitated the evaluation of the contribution of historical demographic processes to genetic structure. A common pattern of past unstable demography (i.e., historical fluctuation in the effective population size) by several Anopheles species, regardless of methodology (DNA markers), mosquito ecology (anthropophilic vs zoophilic), vector status (primary vs secondary) and geographical distribution, suggests that Pleistocene environmental changes were major drivers of divergence at population and species levels worldwide. PMID:21864721

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

2012-01-01

152

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV1  

Microsoft Academic Search

BACKGROUND: Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. RESULTS: We

Charles TT Edwards; Edward C Holmes; Daniel J Wilson; Raphael P Viscidi; Elaine J Abrams; Rodney E Phillips; Alexei J Drummond

2006-01-01

153

Genetic diversity of Clostridium perfringens type A isolates from animals, food poisoning outbreaks and sludge  

PubMed Central

Background Clostridium perfringens, a serious pathogen, causes enteric diseases in domestic animals and food poisoning in humans. The epidemiological relationship between C. perfringens isolates from the same source has previously been investigated chiefly by pulsed-field gel electrophoresis (PFGE). In this study the genetic diversity of C. perfringens isolated from various animals, from food poisoning outbreaks and from sludge was investigated. Results We used PFGE to examine the genetic diversity of 95 C. perfringens type A isolates from eight different sources. The isolates were also examined for the presence of the beta2 toxin gene (cpb2) and the enterotoxin gene (cpe). The cpb2 gene from the 28 cpb2-positive isolates was also partially sequenced (519 bp, corresponding to positions 188 to 706 in the consensus cpb2 sequence). The results of PFGE revealed a wide genetic diversity among the C. perfringens type A isolates. The genetic relatedness of the isolates ranged from 58 to 100% and 56 distinct PFGE types were identified. Almost all clusters with similar patterns comprised isolates with a known epidemiological correlation. Most of the isolates from pig, horse and sheep carried the cpb2 gene. All isolates originating from food poisoning outbreaks carried the cpe gene and three of these also carried cpb2. Two evolutionary different populations were identified by sequence analysis of the partially sequenced cpb2 genes from our study and cpb2 sequences previously deposited in GenBank. Conclusion As revealed by PFGE, there was a wide genetic diversity among C. perfringens isolates from different sources. Epidemiologically related isolates showed a high genetic similarity, as expected, while isolates with no obvious epidemiological relationship expressed a lesser degree of genetic similarity. The wide diversity revealed by PFGE was not reflected in the 16S rRNA sequences, which had a considerable degree of sequence similarity. Sequence comparison of the partially sequenced cpb2 gene revealed two genetically different populations. This is to our knowledge the first study in which the genetic diversity of C. perfringens isolates both from different animals species, from food poisoning outbreaks and from sludge has been investigated. PMID:16737528

Johansson, Anders; Aspan, Anna; Bagge, Elisabeth; Baverud, Viveca; Engstrom, Bjorn E; Johansson, Karl-Erik

2006-01-01

154

Synthetic biology: advancing the design of diverse genetic systems  

PubMed Central

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

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

2013-01-01

155

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

PubMed Central

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

Hellmair, Michael; Kinziger, Andrew P.

2014-01-01

156

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

PubMed Central

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

Bell, J.J; Okamura, B

2005-01-01

157

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

PubMed Central

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

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

2010-01-01

158

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

PubMed

Oenocarpus mapora is an Amazonian palm species commonly used by native populations for food and in folk medicine. We measured genetic variability, using RAPD markers, of material kept in a germplasm bank composed of accessions sampled from the Brazilian Amazon. These included 74 individuals from 23 accessions sampled from 9 localities in three States of the Brazilian Amazon. Jaccard genetic similarities were calculated based on 137 polymorphic bands, amplified by 15 primers. Dendrograms constructed based on the genetic similarities among individuals and sample localities demonstrated genetic separation of Acre State from the States of Amazonas and Pará. Two models in three hierarchical levels were considered for AMOVA: one considering the grouping of sampling sites in each state, and the other considering sampling sites in each subgroup formed by the dendrograms. The first model showed no significant genetic variation among states. On the other hand, genetic variation among subgroups was significant. In this model, the within-sample-site genetic diversity was 47.15%, which is considered to be low, since O. mapora is allogamous. By means of Bayesian analysis, the sample sites were clustered into five groups, and their distribution was similar to what we found in the dendrograms based on genetic similarity. PMID:23212338

Moura, E F; de Oliveira, M S P

2012-01-01

159

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

PubMed

The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers in 236 samples. All estimated loci were very polymorphic indicated by high values of polymorphism information content (from 0.76 in S0225 to 0.92 in Sw2410). Indigenous populations had very high level of genetic diversity (mean He = 0.75); of all indigenous breeds, Lung Pu showed highest mean number of alleles (MNA = 10.1), gene diversity (He = 0.82), allele richness (5.33) and number of private alleles (10). Thirteen percentage of the total genetic variation observed was due to differences among populations. The neighbour-joining dendrogram obtained from Nei's standard genetic distance differentiated eight populations into four groups including Yorkshire, two wild populations, Mong Cai population and a group of four other indigenous populations. The Bayesian clustering with the admixture model implemented in Structure 2.1 indicated seven possible homogenous clusters among eight populations. From 79% (Ha Lang) to 98% (Mong Cai). individuals in indigenous pigs were assigned to their own populations. The results confirmed high level of genetic diversity and shed a new light on genetic structure of Vietnam indigenous pig populations. PMID:24373066

Pham, L D; Do, D N; Nam, L Q; Van Ba, N; Minh, L T A; Hoan, T X; Cuong, V C; Kadarmideen, H N

2014-10-01

160

Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite  

PubMed Central

Given the growing appreciation of serious health sequelae from widespread Trichomonas vaginalis infection, new tools are needed to study the parasite's genetic diversity. To this end we have identified and characterized a panel of 21 microsatellites and six single-copy genes from the T. vaginalis genome, using seven laboratory strains of diverse origin. We have (1) adapted our microsatellite typing method to incorporate affordable fluorescent labeling, (2) determined that the microsatellite loci remain stable in parasites continuously cultured up to 17 months, and (3) evaluated microsatellite marker coverage of the six chromosomes that comprise the T. vaginalis genome using fluorescent in situ hybridization (FISH). We have used the markers to show that T. vaginalis is a genetically diverse parasite in a population of commonly used laboratory strains. In addition, we have used phylogenetic methods to infer evolutionary relationships from our markers in order to validate their utility in future population analyses. Our panel is the first series of robust polymorphic genetic markers for T. vaginalis that can be used to classify and monitor lab strains, as well as provide a means to measure the genetic diversity and population structure of extant and future T. vaginalis isolates. PMID:20813140

Conrad, Melissa; Zubacova, Zuzana; Dunn, Linda A.; Upcroft, Jacqui; Sullivan, Steven A.; Tachezy, Jan; Carlton, Jane M.

2010-01-01

161

Cryptic genetic diversity and complex phylogeography of the boreal North American scorpion, Paruroctonus boreus (Vaejovidae).  

PubMed

Diverse studies in western North America have revealed the role of topography for dynamically shaping genetic diversity within species though vicariance, dispersal and range expansion. We examined patterns of phylogeographical diversity in the widespread but poorly studied North American vaejovid scorpion, Paruroctonus boreus Girard 1854. We used mitochondrial sequence data and parsimony, likelihood, and Bayesian inference to reconstruct phylogenetic relationships across the distributional range of P. boreus, focusing on intermontane western North America. Additionally, we developed a species distribution model to predict its present and historical distributions during the Last Glacial Maximum and the Last Interglacial Maximum. Our results documented complex phylogeographic relationships within P. boreus, with multiple, well-supported crown clades that are either geographically-circumscribed or widespread and separated by short, poorly supported internodes. We also observed subtle variation in predicted habitat suitability, especially at the northern, eastern and southern edges of the predicted distributional range under past climatic conditions. The complex phylogenetic relationships of P. boreus suggests that historical isolation and expansion of populations may have occurred. Variation in the predicted distributional range over time may implicate past climatic fluctuations in generating the patterns of genetic diversity observed in P. boreus. These findings highlight both the potential for cryptic biodiversity in widespread North American scorpion species and the importance of phylogeographical studies for understanding the factors responsible for generating the biodiversity of western North America. PMID:24269314

Miller, A L; Makowsky, R A; Formanowicz, D R; Prendini, L; Cox, C L

2014-02-01

162

Genetic diversity of Microcystis cyanophages in two different freshwater environments.  

PubMed

Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host's phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes. PMID:24671440

Nakamura, Ginji; Kimura, Shigeko; Sako, Yoshihiko; Yoshida, Takashi

2014-06-01

163

Genetic diversity affects colony survivorship in commercial honey bee colonies  

NASA Astrophysics Data System (ADS)

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.

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

2013-08-01

164

Genetic diversity in Leavenworthia populations with different inbreeding levels.  

PubMed Central

Levels of neutral genetic diversity within and between populations were compared between outcrossing (self-incompatible) and inbreeding populations in the annual plant genus Leavenworthia. Two taxonomically independent comparisons are possible, since self-incompatibility has been lost twice in the group of species studied. Within inbred populations of L.uniflora and L.crassa, no DNA sequence variants were seen among the alleles sampled, but high diversity was seen in alleles from populations of the outcrosser L. stylosa, and in self-incompatible L. crassa populations. Diversity between populations was seen in all species. Although total diversity values were lower in the sets of inbreeding populations, between-population values were as high or higher, than those in the outcrossing taxa. Possible reasons for these diversity patterns are discussed. As the effect of inbreeding appears to be a greater than twofold reduction in diversity, we argue that some process such as selection for advantageous mutations, or against deleterious mutations, or bottlenecks occurring predominantly in the inbreeders, appears necessary to account for the findings. If selection for advantageous mutations is responsible, it appears that it must be some form of local adaptive selection, rather than substitution of alleles that are advantageous throughout the species. This is consistent with the finding of high between-population diversity in the inbreeding taxa. PMID:9523432

Liu, F; Zhang, L; Charlesworth, D

1998-01-01

165

Genetic variation and relationships of eighteen Chinese indigenous pig breeds  

Microsoft Academic Search

Chinese indigenous pig breeds are recognized as an invaluable component of the world's pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types,

Shu-Lin Yang; Zhi-Gang Wang; Bang Liu; Gui-Xiang Zhang; Shu-Hong Zhao; Mei Yu; Bin Fan; Meng-Hua Li; Tong-An Xiong; Kui Li

2003-01-01

166

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

PubMed Central

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

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

2013-01-01

167

Genetic diversity of Mycosphaerella graminicola isolates from a single field.  

PubMed

Septoria tritici blotch caused by Mycosphaerella graminicola is currently one of the most economically damaging diseases on wheat crops worldwide. Two hundred and sixty single-conidial isolates of this fungus were sampled in April 2012 in the Nord-Pas de Calais region (France). They have all been collected from 13 distinct plots in a single field. The corresponding isolates were then fingerprinted using 8 microsatellite markers in order to assess the genetic diversity and population structure of M. graminicola at the single field scale. The results revealed a high genotypic diversity within the collected population, with the detection of 83% of unique haplotypes among the isolates tested (clonal fraction = 17%). A high genic diversity was also found as indicated by the Nei's index value (0.50) and strong allele diversity obtained (number of alleles per locus ranged from 7 to 17, with an average of 10 alleles per locus). Further analyses showed a low population differentiation (G(ST) = 0.08) and a high gene flow (Nm = 5.64) between the 13 sampled plots. Our study suggests that sexual reproduction, by its frequency, plays a major role in the genetic diversification of M. graminicola at the field level and in the distribution and homogenization of this diversity in the field via wind-born ascospores. PMID:25151819

Siah, A; Reignault, Ph; Halama, P

2013-01-01

168

Turtle Carapace Anomalies: The Roles of Genetic Diversity and Environment  

PubMed Central

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

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

2011-01-01

169

Examining Relationships Between Social-Emotional, Cultural, and Academic Outcomes of Culturally Diverse Adolescents  

E-print Network

early adolescents: Mediated relationships to academicsignificant relationships, where adolescents who reportRelationships Between Social-Emotional, Cultural, and Academic Outcomes of Culturally Diverse Adolescents

Garcia, Nicole Marie

2011-01-01

170

Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata.  

PubMed

The reconstruction of recent historical population sizes allowed us to investigate the influence of random evolutionary processes on present-day genetic diversity in populations of Dryopteris cristata. This long-lived, allotetraploid fern is rare and endangered in the study area at the southwestern border of its European distribution. Random amplified polymorphic DNA (RAPD) diversity of 280 individuals from 14 populations of D. cristata was extraordinarily low, suggesting an ancient bottleneck in the species' history. Analysis of molecular variance (AMOVA) of 25 different RAPD multiband phenotypes revealed significant genetic variation among three geographical regions (15%) and among populations within regions (34%); 51% of total variance was attributed to variation within populations. High population differentiation indicated limited gene flow among populations, and genetic divergence was not correlated with geographical distance. There was no relationship between genetic variation within population, estimated as molecular variance, and present-day population size. Populations with recent historical bottlenecks of fewer than 25 individuals showed a substantial and significant reduction in genetic variation, compared with populations without bottlenecks. Comparatively high levels of genetic variation were still maintained in small remnants (60-110 individuals) of formerly large populations. Average deviations of frequencies of widespread polymorphic markers within populations from their frequencies in the whole dataset were significantly higher in small or recently bottlenecked populations than in constantly large populations, thus providing evidence for random sampling effects during genetic bottlenecks and drift in small populations. The present investigation demonstrates the importance of population history for understanding present-day genetic diversity within natural populations, as well as for conservation biology. PMID:11737281

Landergott, U; Holderegger, R; Kozlowski, G; Schneller, J J

2001-09-01

171

Genetic Diversity, Population Structure and Wolbachia Infection Status in a Worldwide Sample of Drosophila  

E-print Network

Genetic Diversity, Population Structure and Wolbachia Infection Status in a Worldwide Sample in the development of population genetic models that serve to explain patterns of diversity in natural populations estimated levels of genetic diversity within, and divergence between, these populations, and looked

172

Steelhead Genetic Diversity at Multiple Spatial Scales in a Managed Basin: Snake River, Idaho  

Microsoft Academic Search

We investigated the genetic diversity of steelhead Oncorhynchus mykiss in 74 wild populations and 5 hatchery stocks in Idaho's Snake River basin at the drainage, watershed, and population spatial scales using 11 microsatellite loci. We found significant genetic diversity at multiple spatial scales. Analysis of molecular variance showed that genetic diversity was greater among watersheds within drainages (3.66%) than among

Jennifer L. Nielsen; Alan Byrne; Sara L. Graziano; Christine C. Kozfkay

2009-01-01

173

Isolation of Genetically Diverse Marburg Viruses from Egyptian Fruit Bats  

PubMed Central

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

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

174

Low worldwide genetic diversity in the basking shark (Cetorhinus maximus)  

PubMed Central

The basking shark (Cetorhinus maximus) is found in temperate waters throughout the world's oceans, and has been subjected to extensive exploitation in some regions. However, little is known about its current abundance and genetic status. Here, we investigate the diversity of the mitochondrial DNA control region among samples from the western North Atlantic, eastern North Atlantic, Mediterranean Sea, Indian Ocean and western Pacific. We find just six haplotypes defined by five variable sites, a comparatively low genetic diversity of ?=0.0013 and no significant differentiation between ocean basins. We provide evidence for a bottleneck event within the Holocene, estimate an effective population size (Ne) that is low for a globally distributed species, and discuss the implications. PMID:17148309

Rus Hoelzel, A; Shivji, Mahmood S; Magnussen, Jennifer; Francis, Malcolm P

2006-01-01

175

The Impact of Relationship Education on Adolescents of Diverse Backgrounds  

ERIC Educational Resources Information Center

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.…

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

2007-01-01

176

Structural Diversity and Close Interracial Relationships in College  

ERIC Educational Resources Information Center

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…

Bowman, Nicholas A.

2012-01-01

177

Genetic diversity among watermelon ( Citrullus lanatus and Citrullus colocynthis ) accessions  

Microsoft Academic Search

Genetic diversity was estimated among 42 U.S. PlantIntroduction (PI) accessions of the genusCitrullus (of these, 34 PIs are reported tohave disease resistance), and 5 watermelon cultivars, using 30RAPD primers. These primers produced 662 RAPD markers that could berated with high confidence. Based on these markers, geneticsimilarity coefficients were calculated and a dendrogram wasconstructed using the unweighted pair-group method witharithmetic average

Amnon Levi; Claude E. Thomas; Anthony P. Keinath; Todd C. Wehner

2001-01-01

178

Genetic Diversity of Cylindrospermopsis Strains (Cyanobacteria) Isolated from Four Continents†  

PubMed Central

The genetic diversity of Cylindrospermopsis strains (cyanobacteria) was examined using mainly the 16S-23S internally transcribed spacer (ITS1) sequences. Strains were grouped in three clusters: (i) America, (ii) Europe, and (iii) Africa and Australia. These results suggested a recent spread of Cylindrospermopsis across the American and European continents from restricted warm refuge areas instead of exchanges between continents. On the other hand, they also suggested a recent colonization of Australia by African strains. PMID:15691973

Gugger, Muriel; Molica, Renato; Le Berre, Brigitte; Dufour, Philippe; Bernard, Cecile; Humbert, Jean-Francois

2005-01-01

179

Genetic Diversity in Cymophyllus fraserianus (Cyperaceae), a Rare Monotypic Genus  

Microsoft Academic Search

Cymophyllus fraserianus(Fraser's sedge) is a rare perennial evergreen herb found in late-successional forest communities in the Appalachian Mountains of the U.S. Genetic diversity was assessed at 19 allozyme loci for 12 populations sampled from the southern and central portions of the range of this primitive monotypic genus. Species variation was comparable to that found for other narrowly distributed species, although

Mary Jo W. Godt; J. L. Hamrick; Albert Meier

2004-01-01

180

Genetic and phenotypic diversity in breast tumor metastases.  

PubMed

Metastatic disease is the main cause of cancer-related mortality due to almost universal therapeutic resistance. Despite its high clinical relevance, our knowledge of how cancer cell populations change during metastatic progression is limited. Here, we investigated intratumor genetic and phenotypic heterogeneity during metastatic progression of breast cancer. We analyzed cellular genotypes and phenotypes at the single cell level by performing immunoFISH in intact tissue sections of distant metastatic tumors from rapid autopsy cases and from primary tumors and matched lymph node metastases collected before systemic therapy. We calculated the Shannon index of intratumor diversity in all cancer cells and within phenotypically distinct cell populations. We found that the extent of intratumor genetic diversity was similar regardless of the chromosomal region analyzed, implying that it may reflect an inherent property of the tumors. We observed that genetic diversity was highest in distant metastases and was generally concordant across lesions within the same patient, whereas treatment-naïve primary tumors and matched lymph node metastases were frequently genetically more divergent. In contrast, cellular phenotypes were more discordant between distant metastases than primary tumors and matched lymph node metastases. Diversity for 8q24 was consistently higher in HER2(+) tumors compared with other subtypes and in metastases of triple-negative tumors relative to primary sites. We conclude that our integrative method that couples ecologic models with experimental data in human tissue samples could be used for the improved prognostication of patients with cancer and for the design of more effective therapies for progressive disease. PMID:24448237

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

2014-03-01

181

Genetic analysis of rice varietal diversity for rice blast control.  

PubMed

Two Indica hybrid rice of Shanyou63 (A) and Shanyou22 (B), two glutinous landraces of Huanghenuo (C) and Zinuo (D) and three improved Japonica rice of Hexi41 (E), Chujing12 (F) and 8126 (G) were selected and their genetic resistance relationship was estimated using resistance gene analogue (RGA). The results showed that there were similar genetic relationships between hybrid varieties at the genetic similarity (GS) of 0.86,and among improved Japonica varieties at the GS of 0.84, while highly genetic diversifications between traditional varieties, Indica and Japonica varieties, traditional and modern variety ( GS:0.45). The results also showed that clustering analysis based on RGA data were generally corresponded to known pedigrees and blast field resistances of the varieties. Based on varietal differences in RGA data and agronomic traits, plot experiments of five mixed-planting combinations of A/C, A/D, B/C, B/D and A/B and two combinations of E/C and E/F/G were conducted in Jianshui and Shiping counties ( Indica rice growing region) and Luxi County (warm Japonica region) in Yunnan Province in past two years, respectively. The results demonstrated that rice blast management was more effective in five mixed-planting combinations of varieties with different genetic backgrounds (GS: 0.45-0.77) than in two combinations with similar genetic relationships (GS: 0.84-0.90), compared with their monocultures. It is evident for the highly susceptible landraces in mixed-planting to achieve disease control, with significant decreases both in incidence and severity. The blast control efficiencies of landraces in different mixture combinations reached to 54.47%-92.18%. The control efficiencies of improved varieties varied from 15.12% to 25.54% in mixture combinations with closed genetic relationship. In addition,the total yield of 5 varietal combinations with distant genetic relationship increased 539.0-904.0 kg/ha in the mixed-planting plots, at increase rates of 5.6%-10.2%. Mixed rice varieties with similar genetic background did not achieve significant yield increase. Otherwise, the yield of E/F/G decreased 2.7%-4.0% compared with pure stand. The results can provide scientific basis of varietal combinations in diversification experiments for blast control. PMID:15473323

Zhu, You-Yong; Sun, Yan; Wang, Yun-Yue; Li, Yan; He, Yue-Qiu; He, Xia-Hong; Mundt, Christopher C; Mew, Tom W; Hei, Leung

2004-07-01

182

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

PubMed Central

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

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

183

Genetic diversity of hydrothermal-vent barnacles in Manus Basin  

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

184

[Genetic diversity in goat breeds based on microsatellite analysis].  

PubMed

Fluorescence PCR was applied to investigate the genetic diversities of 9 indigenous Chinese goat breeds and 1 exotic breed with 10 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations and the International Livestock Research Institute of Animal Genetics, which provide data for the preservation and utilization of indigenous goat breeds genetic resource. We found that the 7 breeds were high polymorphic while 3 breeds were moderate polymorphic. We also detected 119 alleles, and the effective allele number ranged from 1.4641 to 9.2911. The average heterozygosity of loci and breeds respectively varied from 0.2618 to 0.7672 and from 0.5196 to 0.7024. As well as SRCRSP23 site and Hexi cashmere goat had the highest average heterozygosity. Then we analyzed the phylogenetic trees (NJ and UPGMA), and found both of them were generally in accordance with their original breeding history and localities. PMID:20684301

Xu, Limei; Liu, Chousheng; Zhang, Liping; Wang, Zhigang; Han, Xu; Li, Xiaoxia; Chang, Shuang

2010-05-01

185

Genetic diversity and population structure of disjunct Newfoundland and central Ontario  

E-print Network

Genetic diversity and population structure of disjunct Newfoundland and central Ontario populations years presents an opportunity to determine and monitor population bottleneck effects on genetic populations examined. The Newfoundland populations were as genetically variable as those from Ontario

Innes, David J.

186

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

PubMed Central

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

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

187

Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites.  

PubMed

The cultivated diploid, Gossypium arboreum L., (A genome) is an invaluable genetic resource for improving modern tetraploid cotton (G. hirsutum L. and G. barbadense L.) cultivars. The objective of this research is to select a set of informative and robust microsatellites for studying genetic relationships among accessions of geographically diverse G. arboreum cultivars. From more than 1,500 previously developed simple sequence repeat (SSR) markers, 115 genomic (BNL) and EST-derived (MUCS and MUSS) markers were used to evaluate the allelic diversity of a core panel of G. arboreum accessions. These SSR data enabled advanced genome analyses. A set of 25 SSRs were selected based both upon their high level of informativeness (PIC > or = 0.50) and the production of clear PCR bands on agarose gels. Subsequently, 96 accessions representing a wide spectrum of diversity of G. arboreum cultivars were analyzed with these markers. The 25 SSR loci revealed 75 allelic variants (polymorphisms) ranging from 2 to 4 alleles per locus. The Neighborjoining (NJ) method, based on genetic dissimilarities, revealed that cultivars from geographically adjacent countries tend to cluster together. Outcomes of this research should be useful in decreasing redundancy of effort and in constructing a core collection of G. arboreum, important for efficient use of this genetic resource in cotton breeding. PMID:18853261

Kantartzi, Stella K; Ulloa, Mauricio; Sacks, Erik; Stewart, James McD

2009-05-01

188

Genetic Diversity and Pathogenicity of Cylindrocarpon destructans Isolates Obtained from Korean Panax ginseng  

PubMed Central

We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants. PMID:25071387

Song, Jeong Young; Seo, Mun Won; Kim, Sun Ick; Nam, Myeong Hyeon; Lim, Hyoun Sub

2014-01-01

189

[Genetic diversity of Dactylis glomerata germplasm resources detected by Inter-simple Sequence Repeats (ISSRS) molecular markers].  

PubMed

Inter-simple Sequence Repeat (ISSR) molecular markers were used to detect the genetic diversity among 50 materials of Dactylis glomerata collected from China and other countries. Twelve primers produced 101 polymorphic bands, averaged 8.41 bands each primer pair. The average percentage of polymorpgic bands was 86.3.8%, and the range of GS (define) was 0.6116-0.9290, indicating a rich genetic diversity of D. glomerata. Based on the cluster and principal component analyses on the genetic characteristics, D. glomerata could be divided into 5 groups according to the nearest phylogenetic relationship. In most cases, accessions from the same continent were classified into the same group, the accessions from China and the United States belong to the different groups, respectively, indicating the geographical distribution of genetic diversity of D. glomerata. The present paper also discussed collection and conservation of germplasm resources in D. glomerata. PMID:16963418

Zeng, Bing; Zhang, Xin-Quan; Fan, Yan; Lan, Ying; Ma, Xiao; Peng, Yan; Liu, Wei

2006-09-01

190

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

PubMed Central

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

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

2011-01-01

191

Productivity-Diversity Relationships in Lake Plankton Communities  

PubMed Central

One of the most intriguing environmental gradients connected with variation in diversity is ecosystem productivity. The role of diversity in ecosystems is pivotal, because species richness can be both a cause and a consequence of primary production. However, the mechanisms behind the varying productivity-diversity relationships (PDR) remain poorly understood. Moreover, large-scale studies on PDR across taxa are urgently needed. Here, we examined the relationships between resource supply and phyto-, bacterio-, and zooplankton richness in 100 small boreal lakes. We studied the PDR locally within the drainage systems and regionally across the systems. Second, we studied the relationships between resource availability, species richness, biomass and resource ratio (N?P) in phytoplankton communities using Structural Equation Modeling (SEM) for testing the multivariate hypothesis of PDR. At the local scale, the PDR showed variable patterns ranging from positive linear and unimodal to negative linear relationships for all planktonic groups. At the regional scale, PDRs were significantly linear and positive for phyto- and zooplankton. Phytoplankton richness and the amount of chlorophyll a showed a positive linear relationship indicating that communities consisting of higher number of species were able to produce higher levels of biomass. According to the SEM, phytoplankton biomass was largely related to resource availability, yet there was a pathway via community richness. Finally, we found that species richness at all trophic levels was correlated with several environmental factors, and was also related to richness at the other trophic levels. This study showed that the PDRs in freshwaters show scale-dependency. We also documented that the PDR complies with the multivariate model showing that plant biomass is not mirroring merely the resource availability, but is also influenced by richness. This highlights the need for conserving diversity in order to maintain ecosystem processes in freshwaters. PMID:21850218

Korhonen, Jenni J.; Wang, Jianjun; Soininen, Janne

2011-01-01

192

Genetic diversity and adaptedness in tetraploid Avena barbata and its diploid ancestors Avena hirtula and Avena wiestii.  

PubMed

Avena barbata, a tetraploid grass, is much more widely adapted and successful in forming dense stands than its diploid ancestors. The success of such polyploids has often been attributed to heterosis associated with ability to breed true for a highly heterozygous state in which allelic differences between the parents are fixed in the polyploid by chromosome doubling. We have examined the relationship between genetic diversity and adaptedness for 14 allozyme loci in A. barbata and its diploid ancestors in samples collected from diverse habitats in Israel and Spain. The relationship varied from locus to locus: superior adaptedness was associated with genetic uniformity for five loci, in part with genetic uniformity and in part with genetic diversity (monomorphism for a single heteroallelic quadriplex) for one locus, and with allelic diversity in the form of heteroallelic quadriplexes combined with genotypic diversity in the form of complex polymorphisms among different homoallelic and/or heteroallelic quadriplexes for the eight remaining loci. These results indicate that allelic diversity fixed in nonsegregating form through chromosome doubling was an important factor in the evolution of adaptedness in A. barbata. However, it is unlikely that heterosis associated with heterozygosity contributed significantly to superior adaptedness in either the diploids or the tetraploid because virtually all loci (approximately 99%) were homozygous in the Avena diploids and tetraploid. PMID:1996323

García, P; Morris, M I; Sáenz-de-Miera, L E; Allard, R W; Pérez de la Vega, M; Ladizinsky, G

1991-02-15

193

Peach genetic resources: diversity, population structure and linkage disequilibrium  

PubMed Central

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

2013-01-01

194

Limited genetic diversity preceded extinction of the Tasmanian tiger.  

PubMed

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

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

2012-01-01

195

Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger  

PubMed Central

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

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

2012-01-01

196

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

PubMed

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

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

197

Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm  

PubMed Central

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

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

2013-01-01

198

Genetic Diversity of Pectobacterium carotovorum subsp. brasiliensis Isolated in Korea  

PubMed Central

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

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

2014-01-01

199

PCR-based fingerprinting using AFLPs as a tool for studying genetic relationships in Lactuca spp.  

PubMed

AFLP markers were evaluated for determining the phylogenetic relationships Lactuca spp. Genetic distances based on AFLP data were estimated for 44 morphologically diverse lines of cultivated L. sativa and 13 accessions of the wild species L. serriola, L. saligna, L. virosa, L. perennis, and L. indica. The same genotypes were analyzed as in a previous study that had utilized RFLP markers. The phenetic tree based on AFLP data was consistent with known taxonomic relationships and similar to a tree developed with RFLP data. The genetic distance matrices derived from AFLP and RFLP data were compared using least squares regression analysis and, for the cultivar data, by principal component analysis. There was also a positive linear relationship between distance estimates based on AFLP data and kinship coefficients calculated from pedigree data. AFLPs represent reliable PCR-based markers for studies of genetic relationships at a variety of taxonomic levels. PMID:24162531

Hill, M; Witsenboer, H; Zabeau, M; Vos, P; Kesseli, R; Michelmore, R

1996-12-01

200

Genetics and pathophysiology of affective disorders: relationship to fibromyalgia  

Microsoft Academic Search

Summary Depression and fibromyalgia (FM) share common symptoms, indicating a close relationship between both disorders. FM patients frequently present symptoms of major depression. Genetic epidemiological studies show that genetic transmission is one important component. Molecular genetic studies are on the way; the serotonin transporter promoter gene seems to be associated with neurotic anxiety and FM. Biochemical studies related to the

M. Ackenheil

1998-01-01

201

Genetic diversity of Gallibacterium isolates from California turkeys.  

PubMed

The aim of the present study was to investigate the genetic diversity of Gallibacterium isolates recovered from lesions in turkeys. Gallibacterium has been isolated from various bird species including turkeys, but no large investigations have yet been made to characterize isolates from turkeys genetically. We therefore genotyped 53 Gallibacterium isolates obtained from turkeys between 1998 and 2004. Fifty isolates originated from 29 different flocks in California and the remaining three came from three German turkey flocks. All were recovered from birds with lesions, mainly in the upper respiratory tract. Five chicken isolates from California and five Gallibacterium reference strains were also included. Amplified fragment length polymorphism analysis demonstrated substantial genetic diversity among the Gallibacterium isolates. However, we also demonstrated that some Gallibacterium clones were present in consecutive rotations at the same farm during the entire 6-year observation period and were present in different flocks from different farms. Similarly, the same clone was identified from two of the three German flocks. Further investigation of the spread of Gallibacterium between turkey flocks, including infections acquired from chickens or wild birds, should be carried out. PMID:17497336

Bojesen, A M; Shivaprasad, H L

2007-06-01

202

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

PubMed Central

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

Bomcke, Elisabeth; Gengler, Nicolas; Cothran, E. Gus

2011-01-01

203

Using Plant Functional Traits to Explain Diversity–Productivity Relationships  

PubMed Central

Background The different hypotheses proposed to explain positive species richness–productivity 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 Rao’s 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 (40–82% of explained variation) than species richness per se (<1–13% 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

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

2012-01-01

204

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1  

PubMed Central

Background Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. Results We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Conclusion Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission. PMID:16556318

Edwards, Charles TT; Holmes, Edward C; Wilson, Daniel J; Viscidi, Raphael P; Abrams, Elaine J; Phillips, Rodney E; Drummond, Alexei J

2006-01-01

205

Allozyme Diversity in Natural Populations of Viola palmensis Webb & Berth. (Violaceae) from La Palma (Canary Islands): Implications for Conservation Genetics  

PubMed Central

Genetic diversity was measured by allozyme electrophoresis in eight natural populations of the threatened Canarian endemic Viola palmensis Webb & Berth. (Violaceae). Nineteen alleles corresponding to 11 gene loci were detected. High levels of genetic diversity were found, ranging from 36·3 to 45·4 % for the percentage of polymorphic loci (P), from 1·45 to 1·60 for the average number of alleles per locus (A) and from 0·128 to 0·200 for the expected heterozygosity (He). Between 85·5 and 96·6 % of genetic variability was apportioned within populations. As a whole, populations were not at Hardy–Weinberg equilibrium, with a deficit of heterozygous individuals attributable to the existence of genetic structuring in the populations analysed. The levels of interpopulation genetic differentiation were low (mean FST = 0·100), while genetic identity pair?wise comparisons were high (mean I = 0·973) suggesting considerable levels of gene flow among populations. No relationship was detected between genetic differentiation and geographical distances between populations. An outcrossing insect?mediated breeding system might contribute to pollen dispersion of this species. For conservation genetics we suggest in situ preservation areas are defined that are free of disturbance and that include populations with the highest genetic diversity. PMID:12451028

BATISTA, FRANCISCO; SOSA, PEDRO A.

2002-01-01

206

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

PubMed Central

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

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

2011-01-01

207

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

PubMed Central

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

2013-01-01

208

Genetic diversity in black South Africans from Soweto  

PubMed Central

Background Due to the unparalleled genetic diversity of its peoples, Africa is attracting growing research attention. Several African populations have been assessed in global initiatives such as the International HapMap and 1000 Genomes Projects. Notably excluded, however, is the southern Africa region, which is inhabited predominantly by southeastern Bantu-speakers, currently suffering under the dual burden of infectious and non-communicable diseases. Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure. Here, we present the most detailed exploration, to date, of genetic diversity in 94 unrelated southeastern Bantu-speaking South Africans, resident in urban Soweto (Johannesburg). Results Participants were typed for ~4.3 million SNPs using the Illumina Omni5 beadchip. PCA and ADMIXTURE plots were used to compare the observed variation with that seen in selected populations worldwide. Results indicated that Sowetans, and other southeastern Bantu-speakers, are a clearly distinct group from other African populations previously investigated, reflecting a unique genetic history with small, but significant contributions from diverse sources. To assess the suitability of our sample as representative of Sowetans, we compared our results to participants in a larger rheumatoid arthritis case–control study. The control group showed good clustering with our sample, but among the cases were individuals who demonstrated notable admixture. Conclusions Sowetan population structure appears unique compared to other black Africans, and may have clinical implications. Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme. PMID:24059264

2013-01-01

209

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

PubMed Central

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

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

2010-01-01

210

Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia  

PubMed Central

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

Maccari, Marta; Amat, Francisco; Gomez, Africa

2013-01-01

211

How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings  

PubMed Central

Major histocompatibility complex (MHC) genes have been put forward as a model for studying how genetic diversity is maintained in wild populations. Pathogen-mediated selection (PMS) is believed to generate the extraordinary levels of MHC diversity observed. However, establishing the relative importance of the three proposed mechanisms of PMS (heterozygote advantage, rare-allele advantage and fluctuating selection) has proved extremely difficult. Studies have attempted to differentiate between mechanisms of PMS using two approaches: (i) comparing MHC diversity with that expected under neutrality and (ii) relating MHC diversity to pathogen regime. Here, we show that in many cases the same predictions arise from the different mechanisms under these approaches, and that most studies that have inferred one mechanism of selection have not fully considered the alternative explanations. We argue that, while it may be possible to demonstrate that particular mechanisms of PMS are occurring, resolving their relative importance within a system is probably impossible. A more realistic target is to continue to demonstrate when and where the different mechanisms of PMS occur, with the aim of determining their relative importance across systems. We put forward what we believe to be the most promising approaches that will allow us to progress towards achieving this. PMID:20071384

Spurgin, Lewis G.; Richardson, David S.

2010-01-01

212

Molecular characterization and genetic diversity of Prunus rootstocks  

Microsoft Academic Search

Twenty microsatellite primer pairs, previously developed in peach, were used to characterize and to explore genetic relationships among 44 clones, representing three groups of rootstocks defined as: (1) Peach-based rootstocks (Prunus dulcis×P. persica, P. persica×P. davidiana); (2) Myrobalan-Marianna plums (P. cerasifera and interspecific hybrids having P. cerasifera as a parent); and (3) Slow growing plums (P. insititia, P. domestica, and

Mariem Bouhadida; Ana María Casas; María José Gonzalo; Pere Arús; María Ángeles Moreno; Yolanda Gogorcena

2009-01-01

213

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

PubMed

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

Khadivi-Khub, Abdollah

2014-09-01

214

Genetic diversity in populations of Gentoo penguins (Pygoscelis papua).  

PubMed

RAPD analysis was used to examine the extent of genetic polymorphism in two populations of Gentoo penguin (Pygoscelis papua) from Antarctic Islands (Petermann and Livingston). The chosen two of three 10 mer oligonucleotide primers accordingly to preliminary results showed different levels of polymorphism in Gentoo penguins at Petermann Island (from 23.53 to 42.86%) and Livingston Island (from 52.94 to 57.14%). Nei's similarity coefficients were in range from 0.5606 (when Gentoo genome profiles were compared with RAPD profiles of two related penguin species: Pygoscelis adeliae (Adelie) and Pygoscelis antarctica (Chinstrep)) to 0.9281 among observed Gentoo penguin populations. Nei's distances values ranged from 0.0746 to 0.5787 among the populations and species. The obtained results will be used for further estimation of genetic diversity of Gentoo penguins and determination of their taxonomic status. PMID:16865990

Dranitsina, A S; Telegeev, G D; Maliuta, S S; Bezrukov, V F

2006-01-01

215

Genetic diversity of subgroup 1 ilarviruses from Eastern Australia.  

PubMed

This is the first report of the genetic diversity within ilarvirus subgroup 1 from eastern Australia. It supports the separation of tobacco streak virus (TSV) strains from parthenium (Parthenium hysterophorus) and crownbeard (Verbescina encelioides) based on serology and host specificity. It has confirmed one previously described strain of TSV as a member of the species Strawberry necrotic shock virus and another as a new subgroup 1 ilarvirus, ageratum latent virus (AgLV), from Ageratum houstonianum. A multiplex RT-PCR showed that the genetically distinct strains of TSV and AgLV were commonly found in symptomless infections in virus-specific alternative weed hosts growing over a wide geographical range in eastern Australia. TSV has been one of the most damaging viruses in Australian oilseed and pulse crops in recent years, and this study has provided the taxonomic knowledge essential for the development of control programs for these viruses. PMID:23474983

Sharman, M; Thomas, J E

2013-08-01

216

Genetic diversity of 10 X chromosome STRs in northern Portugal  

Microsoft Academic Search

Genetic data of 10 X chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and\\u000a DXS6789) were obtained in a sample of unrelated males born in the five northern Portuguese districts. In a global sample of\\u000a 347 individuals, no shared haplotypes were found for this set of markers and single locus gene diversities were high, varying\\u000a between 0.678

Rui Pereira; Iva Gomes; António Amorim; Leonor Gusmão

2007-01-01

217

Effects of inbreeding on the genetic diversity of populations.  

PubMed Central

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

Charlesworth, Deborah

2003-01-01

218

Effects of metapopulation processes on measures of genetic diversity.  

PubMed Central

Many species persist as a metapopulation under a balance between the local extinction of subpopulations or demes and their recolonization through dispersal from occupied patches. Here we review the growing body of literature dealing with the genetic consequences of such population turnover. We focus our attention principally on theoretical studies of a classical metapopulation with a 'finite-island' model of population structure, rather than on 'continent-island' models or 'source-sink' models. In particular, we concern ourselves with the subset of geographically subdivided population models in which it is assumed that all demes are liable to extinction from time to time and that all demes receive immigrants. Early studies of the genetic effects of population turnover focused on population differentiation, such as measured by F(ST). A key advantage of F(ST) over absolute measures of diversity is its relative independence of the mutation process, so that different genes in the same species may be compared. Another advantage is that F(ST) will usually equilibrate more quickly following perturbations than will absolute levels of diversity. However, because F(ST) is a ratio of between-population differentiation to total diversity, the genetic effects of metapopulation processes may be difficult to interpret in terms of F(ST) on its own, so that the analysis of absolute measures of diversity in addition is likely to be informative. While population turnover may either increase or decrease F(ST), depending on the mode of colonization, recurrent extinction and recolonization is expected always to reduce levels of both within-population and species-wide diversity (piS and piT, respectively). One corollary of this is that piS cannot be used as an unbiased estimate of the scaled mutation rate, theta, as it can, with some assumptions about the migration process, in species whose demes do not fluctuate in size. The reduction of piT in response to population turnover reflects shortened mean coalescent times, although the distribution of coalescence times under extinction colonization equilibrium is not yet known. Finally, we review current understanding of the effect of metapopulation dynamics on the effective population size. PMID:11205346

Pannell, J R; Charlesworth, B

2000-01-01

219

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

PubMed Central

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

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

2011-01-01

220

Genetic Diversity and Gene Flow in the Endangered Dwarf Bear Poppy, Arctomecon humilis (Papaveraceae)  

Microsoft Academic Search

Arctomecon humilis is a critically endangered species endemic to the Moenkopi shale of Washington County, Utah. Recovery plans for the species would be improved by an understanding of genetic diversity and gene flow among its remaining populations. Ten variable isozyme loci were used to calculate genetic diversity statistics for study populations. Westerly populations possessed higher levels of genetic variability than

Loreen Allphin; Michael D. Windham; Kimball T. Harper

1998-01-01

221

Author's personal copy Genetic diversity patterns in Phragmites australis at the population,  

E-print Network

Author's personal copy Genetic diversity patterns in Phragmites australis at the population Abstract Genetic diversity, population structure and interrelationships were investigated in eight with that of a distant population in Romania. Genetic distances between Po Plain clones and geographically distant clones

Schierup, Mikkel Heide

222

Environmental and Climatic Determinants of Molecular Diversity and Genetic Population Structure in a Coenagrionid Damselfly  

Microsoft Academic Search

Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed

Maren Wellenreuther; Rosa A. Sánchez-Guillén; Adolfo Cordero-Rivera; Erik I. Svensson; Bengt Hansson; Daniel Ortiz-Barrientos

2011-01-01

223

The influence of malaria parasite genetic diversity and anaemia on mosquito feeding and fecundity  

E-print Network

The influence of malaria parasite genetic diversity and anaemia on mosquito feeding and fecundity H genetics and infection genetic diversity on the fecundity of mosquitoes carrying malaria parasites parasite Plasmodium chabaudi, or by a mixture of both. Mixed genotype infections reduced mosquito fecundity

Rivero, Ana

224

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

Microsoft Academic Search

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 ( F ST = 0.36), but

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

2001-01-01

225

Characterization of casein gene complex and genetic diversity analysis in Indian goats.  

PubMed

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk. PMID:20379889

Rout, P K; Kumar, A; Mandal, A; Laloe, D; Singh, S K; Roy, R

2010-04-01

226

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

PubMed

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

Vashishtha, Amit; Jehan, Tabassum; Lakhanpaul, Suman

2013-07-01

227

Population structure and genetic diversity of a medicinal plant species Retama raetam in southern Tunisia.  

PubMed

Retama raetam is a stem-assimilating, C3, evergreen, medicinal plant species, desert legume common to arid ecosystems around the Mediterranean basin. This study addresses the genetic diversity and relationship among and within three populations collected from different habitats in southern Tunisia by Random Amplified Polymorphic DNA (RAPD). Estimates of the percentage of polymorphic bands, Shannon's diversity information index and Nei's gene diversity index were determined. Results showed that population from the Island Djerba has the lowest Nei's gene diversity; this also was for Shannon diversity index. An analysis of molecular variance indicated that the majority of variation existed within populations (68%) and that there was significant differentiation among populations (phiPT = 0.316, p < 0.001). Genetic distance (phiPT based values) between pairwise populations ranged from 0.098 to 0.505 and the differentiation between pair-wise populations was significant when individual pairs of populations were compared. Based on the coefficient of gene differentiation (Gst), gene flow (Nm) was estimated and was found to vary from 0.490 to 4.609 between pair-wise populations and 1.42 among populations. The results of UPGMA cluster analysis and PCoA analysis indicated that most variation occurred within populations and that genetic differentiation had happened between populations. These findings are important for a better understanding of the adaptive strategy of R. raetam in southern Tunisia and will be useful for conservation managers to work out an effective strategy to protect this important species. PMID:24783800

Abdellaoui, Raoudha; Yahyaoui, Faouzia; Neffati, Mohamed

2014-01-15

228

Genetic diversity in a world germplasm collection of tall fescue.  

PubMed

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

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

2013-07-01

229

Genetic Diversity in the SIR Model of Pathogen Evolution  

PubMed Central

We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R0(1+s)) is higher than the fitness of the resident strain (R0). We show that this invasion probability is given by the relative increment in R0 of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A. PMID:19287490

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

2009-01-01

230

Genetic diversity in a world germplasm collection of tall fescue  

PubMed Central

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

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

2013-01-01

231

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.  

PubMed

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

Thai, Khoa T D; 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

232

Genetic diversity and admixture patterns in Indian populations.  

PubMed

India is a diverse land whose population holds the history of waves of human dispersal. Recent studies suggest two major ancestral contributions to most of the Indian sub-populations. However, present day Indians are thought to contain huge genetic diversity derived consequent to multiple cultural, linguistic and geographical variations. Genome-wide survey of individuals from current North (N-In) and South (S-In) India along with populations from HapMap Phase III and Indian sub-populations from HUGO Pan-Asian SNP Consortium is performed. Multivariate analysis (MDS and PCA) was carried out after merging data from the current study and other consortia. Indian sub-populations clustered separately from populations of major global geographical regions in MDS and PCA in a loose agglomeration except for two Indian subpopulations clustering near far eastern populations. F(st) values indicated diversity among Indian sub-populations which was substantiated by STRUCTURE analysis suggesting the possibility of additional admixture events. PMID:22892377

Chakrabarti, Biswaroop; Kumar, Sunil; Singh, Randeep; Dimitrova, Nevenka

2012-10-25

233

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

PubMed Central

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

Shen, Dong-Wei; Chen, Xiao-Yong

2012-01-01

234

Habitat loss other than fragmentation per se decreased nuclear and chloroplast genetic diversity in a monoecious tree.  

PubMed

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 F(ST) 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

Zhang, Xin; Shi, Miao-Miao; Shen, Dong-Wei; Chen, Xiao-Yong

2012-01-01

235

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

PubMed Central

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

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

2013-01-01

236

Detecting DNA polymorphism and genetic diversity in Lentil (Lens culinaris Medik.) germplasm: comparison of ISSR and DAMD marker.  

PubMed

Genetic diversity and interrelationships among 31 lentil genotypes were evaluated using 10 Inter-Simple Sequence Repeat (ISSR) and 10 directed amplification of minisatellite DNA region (DAMD) primers. A total of 43 and 48 polymorphic bands were amplified by ISSR and DAMD markers, respectively. Average polymorphism information content (PIC) for ISSR and DAMD markers were 0.37 and 0.41, respectively. All 31 lentil genotypes could be distinguished by ISSR markers into three groups and by DAMD markers into two groups. Various molecular markers show a different efficiency for evaluating DNA polymorphism in lentil and indicate that the patterns of variation are clearly influenced by the genetic marker used. Comparatively, the genetic diversity of examined lentil genotypes by two different marker techniques (ISSR and DAMD) was high and indicated that ISSR and DAMD are effective and promising marker systems for fingerprinting in lentil and give useful information on its genetic relationships. PMID:25320472

Seyedimoradi, Hiva; Talebi, Reza

2014-10-01

237

Beta diversity and the scale-dependence of the productivity-diversity relationship: a test in the Californian serpentine flora  

Microsoft Academic Search

Summary 1 The relationship of productivity to species diversity is usually positive at regional scales, but is often neutral, unimodal or negative at local spatial scales. Recent studies have pointed out that beta diversity, or among-locality and within-region variation in species composition, must therefore tend to increase with productivity. 2 We tested for a positive relationship of productivity to beta

SUSAN HARRISON; KENDI F. DAVIES; HUGH D. SAFFORD; JOSHUA H. VIERS

2006-01-01

238

Testing heterogeneity-diversity relationships in tropical forest restoration.  

PubMed

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

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

2013-10-01

239

Genetic diversity and genetic structure of Northern Goshawk ( Accipiter gentilis ) populations in eastern Japan and Central Asia  

Microsoft Academic Search

Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease\\u000a of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks.\\u000a In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in

Yoshihide Takaki; Takayuki Kawahara; Hisashi Kitamura; Ko-ichi Endo; Takuma Kudo

2009-01-01

240

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

PubMed Central

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

Campbell, Michael C.; Tishkoff, Sarah A.

2010-01-01

241

Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity  

Microsoft Academic Search

Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits) and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's

Solomon Gizaw; Hans Komen; Jack J. WINDIG; Olivier Hanotte; Johan AM van Arendonk

2008-01-01

242

Cryptic diversity of the 'cosmopolitan' harpacticoid copepod Nannopus palustris: genetic and morphological evidence.  

PubMed

Nannopus palustris Brady, 1880 is a free-living widely distributed harpacticoid copepod, which has been formerly assumed to be a single, cosmopolitan but highly variable species. We compared several geographically distant N. palustris populations in terms of their morphology and genetics. Populations from the White Sea (WS), the North Sea (NS), the Black Sea (BS) and two sympatric morphs from South Carolina, USA (SC notched and SC straight morphs), were considered. The NS, BS and to a lesser extent SC notched specimens were morphologically similar and partly coincided to the 'canonical' description of the species. By contrast, WS population showed remarkable anatomical and morphometric peculiarities that correspond to some earlier descriptions. Genetic analyses of mitochondrial (cytochrome b) and nuclear (28S rDNA) genes demonstrated the significant distinctness among WS, both SC and (NS+BS) populations, the latter two being genetically indistinguishable. Concordance between mitochondrial and nuclear gene trees and morphological data supports that N. palustris is in fact composed of several pseudo-sibling species, which are genetically and morphologically divergent. Neither correlation between genetic divergence and geographical distance nor significant intrapopulation diversity was found for these species. Taxonomic status, distribution and phylogenetic relationships of the species within the Nannopus genus need to be reconsidered. A further subdivision of species complexes might have important implications for the analysis of biodiversity of benthic copepods and consequently for the interpretation of their (species-specific) ecological function. PMID:22989315

Garlitska, Lesya; Neretina, Tatyana; Schepetov, Dimitry; Mugue, Nikolai; De Troch, Marleen; Baguley, Jeffrey G; Azovsky, Andrey

2012-11-01

243

Evaluation of genetic diversity among Chinese Pleurotus eryngii cultivars by combined RAPD/ISSR marker.  

PubMed

Pleurotus eryngii (DC. Ex. Fr.) Quél is a rare precious edible fungus which belongs to the family Pleurotaceae. This mushroom has highly nutritional, pharmaceutical, economic and ecological values. In the present study, combined randomly amplified polymorphic DNA (RAPD)/inter-simple sequence repeat (ISSR) was used to assess the genetic diversity of P. eryngii strains cultivated in China. For the RAPD and ISSR analyses, 404 and 392 polymorphic bands were obtained from 32 P. eryngii strains using 28 and 24 selected primers, respectively. A combined RAPD/ISSR dendrogram grouped the 32 strains into five clades with coefficient of 0.770. The comparison of RAPD and ISSR was also elucidated in the present study. The results of our study obtained by combined RAPD/ISSR analysis contributed to a better understanding of the genetic relationships among the P. eryngii strains and provide orientation for the strain improvement of P. eryngii species. PMID:22760248

Wang, Shouxian; Yin, Yonggang; Liu, Yu; Xu, Feng

2012-10-01

244

Genetic Variation and Phylogenetic Relationships of Indian Buffaloes of Uttar Pradesh  

PubMed Central

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

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

2013-01-01

245

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

PubMed

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

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

2014-01-01

246

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

PubMed Central

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

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

2014-01-01

247

107TURTLE CONSERVATION GENETICS WORKING GROUP Genetics Issues Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises  

E-print Network

107TURTLE CONSERVATION GENETICS WORKING GROUP ­ Genetics Issues Defining Turtle Diversity: Proceedings of a Workshop on Genetics, Ethics, and Taxonomy of Freshwater Turtles and Tortoises H. Bradley 4:107­123 · © 2007 by Chelonian Research Foundation Genetic Issues in Freshwater Turtle and Tortoise

Janzen, Fredric

248

Diversity, Epidemiology, and Genetics of Class D ?-Lactamases?  

PubMed Central

Class D ?-lactamase-mediated resistance to ?-lactams has been increasingly reported during the last decade. Those enzymes also known as oxacillinases or OXAs are widely distributed among Gram negatives. Genes encoding class D ?-lactamases are known to be intrinsic in many Gram-negative rods, including Acinetobacter baumannii and Pseudomonas aeruginosa, but play a minor role in natural resistance phenotypes. The OXAs (ca. 150 variants reported so far) are characterized by an important genetic diversity and a great heterogeneity in terms of ?-lactam hydrolysis spectrum. The acquired OXAs possess either a narrow spectrum or an expanded spectrum of hydrolysis, including carbapenems in several instances. Acquired class D ?-lactamase genes are mostly associated to class 1 integron or to insertion sequences. PMID:19721065

Poirel, Laurent; Naas, Thierry; Nordmann, Patrice

2010-01-01

249

Genetic diversity of Gallibacterium anatis isolates from different chicken flocks.  

PubMed

Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal. PMID:12791918

Bojesen, Anders Miki; Torpdahl, Mia; Christensen, Henrik; Olsen, John Elmerdahl; Bisgaard, Magne

2003-06-01

250

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

SciTech Connect

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.

Leonard, T. [Univ. of Cincinnati, OH (United States); Roth, A.; Gordon, D.; Wessendarp, T.; Smith, M.K. [Environmental Protection Agency, Cincinnati, OH (United States); Silbiger, R. [Dyncorp, Cincinnati, OH (United States); Torsella, J. [Oak Ridge Inst. of Science, Cincinnati, OH (United States)

1995-12-31

251

Genetic diversity of Echinococcus granulosus in center of Iran.  

PubMed

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

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

2014-08-01

252

Genetic Diversity of Echinococcus granulosus in Center of Iran  

PubMed Central

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.

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

2014-01-01

253

Variation of Genetic Diversity in a Rapidly Expanding Population of the Greater Long-Tailed Hamster (Tscherskia triton) as Revealed by Microsatellites  

PubMed Central

Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984–1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn. PMID:23349815

Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin

2013-01-01

254

Genetic diversity and chemical polymorphism of some Thymus species.  

PubMed

To ascertain whether there are chemical and genetic relationships among some Thymus species and also to determine correlation between these two sets of data, the essential-oil composition and genetic variability of six populations of Thymus including: T. daenensis ?ELAK. (two populations), T. fallax FISCH. & C.A.MEY., T. fedtschenkoi RONNIGER, T. migricus KLOKOV & DES.-SHOST., and T. vulgaris L. were analyzed by GC and GC/MS, and also by randomly amplified polymorphic DNA (RAPD). Thus, 27 individuals were analyzed using 16 RAPD primers, which generated 264 polymorphic scorable bands and volatiles isolated by distillation extraction were subjected to GC and GC/MS analyses. The yields of oils ranged from 2.1 to 3.8% (v/w), and 34 components were identified, amounting to a total percentage of 97.8-99.9%. RAPD Markers allowed a perfect distinction between the different species based on their distinctive genetic background. However, they did not show identical clustering with the volatile-oil profiles. PMID:23776024

Rustaiee, Ali Reza; Yavari, Alireza; Nazeri, Vahideh; Shokrpour, Majid; Sefidkon, Fatemeh; Rasouli, Musa

2013-06-01

255

Genetic and Functional Diversity of Pseudomonas aeruginosa Lipopolysaccharide  

PubMed Central

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

Lam, Joseph S.; Taylor, Veronique L.; Islam, Salim T.; Hao, Youai; Kocincova, Dana

2011-01-01

256

Internal Lattice Reconfiguration for Diversity Tuning in Cellular Genetic Algorithms  

PubMed Central

Cellular Genetic Algorithms (cGAs) have attracted the attention of researchers due to their high performance, ease of implementation and massive parallelism. Maintaining an adequate balance between exploitative and explorative search is essential when studying evolutionary optimization techniques. In this respect, cGAs inherently possess a number of structural configuration parameters that are able to sustain diversity during evolution. In this study, the internal reconfiguration of the lattice is proposed to constantly or adaptively control the exploration-exploitation trade-off. Genetic operators are characterized in their simplest form since algorithmic performance is assessed on implemented reconfiguration mechanisms. Moreover, internal reconfiguration allows the adjacency of individuals to be maintained. Hence, any improvement in performance is only a consequence of topological changes. Two local selection methods presenting opposite selection pressures are used in order to evaluate the influence of the proposed techniques. Problems ranging from continuous to real world and combinatorial are tackled. Empirical results are supported statistically in terms of efficiency and efficacy. PMID:22859973

Morales-Reyes, Alicia; Erdogan, Ahmet T.

2012-01-01

257

Genetic diversity among sea otter isolates of Toxoplasma gondii  

USGS Publications Warehouse

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.

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

2008-01-01

258

Genetic diversity of pestivirus isolates in cattle from Western Austria.  

PubMed

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

Hornberg, Andrea; Fernández, Sandra Revilla; Vogl, Claus; Vilcek, Stefan; Matt, Monika; Fink, Maria; Köfer, Josef; Schöpf, Karl

2009-03-30

259

Spatial Distribution of Genetic Diversity in Wild Populations of Phaseolus vulgaris L. from Guanajuato and Michoacán, Méexico  

Microsoft Academic Search

The diversity, genetic structure, and genetic flow of wild populations of Phaseolus vulgaris L. within its Mesoamerican area of domestication, were analyzed by means of morphological and inter-simple sequence repeat molecular markers. Overall, 89% of the loci studied were polymorphic, 35% in the least diverse population and 65% in the most diverse. Genetic diversity in the populations was high, between

Emeterio Payrode la Cruz; Paul Gepts; Patricia Colunga GarciaMarín; Daniel Zizumbo Villareal

2005-01-01

260

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

PubMed

African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics. PMID:24244771

Duffy, Craig W; MacLean, Lorna; Sweeney, Lindsay; Cooper, Anneli; Turner, C Michael R; Tait, Andy; Sternberg, Jeremy; Morrison, Liam J; MacLeod, Annette

2013-11-01

261

Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat  

PubMed Central

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

2013-01-01

262

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

PubMed Central

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

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

2014-01-01

263

REFINING GENETICALLY INFERRED RELATIONSHIPS USING TREELET COVARIANCE SMOOTHING1  

PubMed Central

Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic investigations is familial relationships. Close relatives can be identified from family records, and more distant relatives can be inferred from large panels of genetic markers. Unfortunately these empirical estimates can be noisy, especially regarding distant relatives. We propose a new method for denoising genetically—inferred relationship matrices by exploiting the underlying structure due to hierarchical groupings of correlated individuals. The approach, which we call Treelet Covariance Smoothing, employs a multiscale decomposition of covariance matrices to improve estimates of pairwise relationships. On both simulated and real data, we show that smoothing leads to better estimates of the relatedness amongst distantly related individuals. We illustrate our method with a large genome-wide association study and estimate the “heritability” of body mass index quite accurately. Traditionally heritability, defined as the fraction of the total trait variance attributable to additive genetic effects, is estimated from samples of closely related individuals using random effects models. We show that by using smoothed relationship matrices we can estimate heritability using population-based samples. Finally, while our methods have been developed for refining genetic relationship matrices and improving estimates of heritability, they have much broader potential application in statistics. Most notably, for error-in-variables random effects models and settings that require regularization of matrices with block or hierarchical structure. PMID:24587841

Crossett, Andrew; Lee, Ann B.; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn

2013-01-01

264

Genetic Relationships of Ethnic Minorities in Southwest China Revealed by Microsatellite Markers  

PubMed Central

Population migrations in Southwest and South China have played an important role in the formation of East Asian populations and led to a high degree of cultural diversity among ethnic minorities living in these areas. To explore the genetic relationships of these ethnic minorities, we systematically surveyed the variation of 10 autosomal STR markers of 1,538 individuals from 30 populations of 25 ethnic minorities, of which the majority were chosen from Southwest China, especially Yunnan Province. With genotyped data of the markers, we constructed phylogenies of these populations with both DA and DC measures and performed a principal component analysis, as well as a clustering analysis by structure. Results showed that we successfully recovered the genetic structure of analyzed populations formed by historical migrations. Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation. PMID:20360948

Zhang, Feng; Huang, Xiaoqin; Lin, Keqin; Shi, Lei; Hu, Songnian; Chu, Jiayou; Wang, Duen-Mei

2010-01-01

265

Assessment of genetic diversity of Bermudagrass (Cynodon dactylon) using ISSR markers.  

PubMed

Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard's similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them. PMID:22312259

Farsani, Tayebeh Mohammadi; Etemadi, Nematollah; Sayed-Tabatabaei, Badraldin Ebrahim; Talebi, Majid

2012-01-01

266

Assessment of Genetic Diversity of Bermudagrass (Cynodon dactylon) Using ISSR Markers  

PubMed Central

Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard’s similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them. PMID:22312259

Farsani, Tayebeh Mohammadi; Etemadi, Nematollah; Sayed-Tabatabaei, Badraldin Ebrahim; Talebi, Majid

2012-01-01

267

Genetic Relationships among Populations of Florida Bass  

Microsoft Academic Search

Florida bass Micropterus floridanus are endemic to peninsular Florida and co-occur with largemouth bass M. salmoides in a natural intergrade zone in the northern portions of the state. In this study, we resolved the genetic population structure among populations of largemouth bass, Florida bass, and their interspecific hybrids from 48 lakes and streams across Florida, and we updated and refined

Brandon L. Barthel; Dijar J. Lutz-Carrillo; Kristen E. Norberg; Wesley F. Porak; Michael D. Tringali; Todd W. Kassler; William E. Johnson; Anne M. Readel; Richard A. Krause; David P. Philipp

2010-01-01

268

Genetic relationships within Brassica rapa as inferred from AFLP fingerprints  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) markers were employed to assess the genetic diversity amongst two large collections of Brassica rapa accessions. Collection A consisted of 161 B. rapa accessions representing different morphotypes among the cultivated B. rapa, including traditional and modern cultivars and breeding materials from geographical locations from all over the world and two Brassica napus accessions. Collection B consisted of

Jianjun Zhao; Xiaowu Wang; Bo Deng; Ping Lou; Jian Wu; Rifei Sun; Zeyong Xu; Jaap Vromans; Maarten Koornneef; Guusje Bonnema

2005-01-01

269

Coppice forests and genetic diversity: A case study in Quercus pyrenaica Willd. from Central Spain  

Microsoft Academic Search

The amount of standing genetic diversity found in oak coppice forests has been subjected to intense debate amongst forest ecologists and managers. In this study, the level of vegetative propagation and the genetic diversity found in a coppice forest of rebollo oak (Quercus pyrenaica) was examined. The current range of rebollo oak in the Iberian Peninsula reveals its adaptation to

M. Valbuena-Carabaña; S. C. González-Martínez; L. Gil

2008-01-01

270

Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep  

Microsoft Academic Search

The rapid expansion of road networks has reduced connectivity among populations of flora and fauna. The resulting isolation is assumed to increase population extinction rates, in part because of the loss of genetic diversity. However, there are few cases where loss of genetic diversity has been linked directly to roads or other barriers. We analysed the effects of such barriers

Clinton W. Epps; John D. Wehausen; George K. Roderick; Rob R. Ramey II; Dale R. McCullough

2005-01-01

271

Genetic diversity of fringed brome ( Bromus ciliatus ) as determined by amplified fragment length polymorphism  

Microsoft Academic Search

Fringed brome (Bromus ciliatus L.) is found in native stands throughout a large area of North America. Little is known about the genetic diversity of this species. The amplified fragment length polymorphism (AFLP) technique was applied to assess the genetic diversity of 16 fringed brome populations sampled in Canada from the provinces of Alberta, British Columbia, Quebec, and Saskatchewan. Four

Yong-Bi Fu; Bruce E. Coulman; Yasas S. N. Ferdinandez; Jacques Cayouette; Paul M. Peterson

2005-01-01

272

Genotypic and Genetic Diversity of the Common Weed Cirsium arvense (Asteraceae)  

Microsoft Academic Search

In many clonal species, seedling establishment is restricted to early successional stages when recruitment is still possible. Then, one expects that adapted genotypes become dominant and genotypic and genetic diversity should decrease with time. We investigated genotypic and genetic diversity within recently founded and established populations of the common weed Cirsium arvense. We used highly polymorphic amplified fragments length polymorphism

Magali Sole; Walter Durka; Sabine Eber; Roland Brandlz

2004-01-01

273

Copyright 2004 by the Genetics Society of America Nucleotide Diversity in Gorillas  

E-print Network

, including past to suggest a much higher level of mtDNA variation in changes in population size, effects of genetic diversity have been con- had the least amount of mtDNA variation among the ducted on humans (e of social structure great apes than in humans. In that study, the mtDNA on genetic diversity, patterns

Seaman, Michael I.

274

Genetic diversity of bitter gourd ( Momordica charantia L.) genotypes revealed by RAPD markers and agronomic traits  

Microsoft Academic Search

Bitter gourd or bitter melon (Momordica charantia L.) is considered as minor cucurbitaceous vegetable in spite of having considerable nutritional and medicinal properties. Although some reports on genetic diversity based on morphological characterization are available, no work has been conducted to estimate genetic diversity using molecular markers in this crop. In the present study, 38 genotypes of M. charantia including

S. S. Dey; A. K. Singh; D. Chandel; T. K. Behera

2006-01-01

275

Genetic diversity, asymmetrical aggression, and recognition in a widespread invasive species  

E-print Network

Genetic diversity, asymmetrical aggression, and recognition in a widespread invasive species Neil D of aggression. This selection, in concert with reductions in genetic diversity after a founder event, likely of relatives, individuals that direct altruistic behavior toward group members can also increase their indirect

Suarez, Andrew V.

276

Diversity of trematode genetic clones within amphipods and the timing of same-clone infections  

Microsoft Academic Search

The genetic diversity of trematodes within second intermediate hosts has important implications for the evolution of trematode populations as these hosts are utilized after the parasites reproduce asexually within first intermediate hosts and before sexual reproduction within definitive hosts. We characterised the genetic clonal diversity of the marine trematode Maritrema novaezealandensis within amphipod (Paracalliope novizealandiae) second intermediate hosts using four

Devon B. Keeney; Jonathan M. Waters; Robert Poulin

2007-01-01

277

Global relationship between phytoplankton diversity and productivity in the ocean  

PubMed Central

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

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

2014-01-01

278

Genetic and evolutionary relationships among Asian Macaques  

Microsoft Academic Search

Published gene frequency data, checked for consistency of allele definitions across laboratories and for comparability of\\u000a geographically identical samples, were pooled into a data set containing frequencies at nine loci for each of 20 populations\\u000a that encompassed 10 macaque species. Genetic distances were calculated by the methods of Kidd and Cavalli-Sforza (1974). These\\u000a distances were used to construct phylogenetic trees

Don J. Melnick; Kenneth K. Kidd

1985-01-01

279

How does genetic diversity change towards the range periphery? An empirical and theoretical test  

Microsoft Academic Search

Question: How does genetic diversity change as one moves along a species' range, towards the periphery? Previous work shows contradictory evidence for an increase, decrease or no clear trend along the range. Hypothesis: A hump-shaped unimodal pattern of within-population genetic diversity will occur along the range with peak diversity in sub-peripheral populations. This hypothesis incorporates and explains some of the

Salit Kark; Lilach Hadany; Uriel N. Safriel; Imanuel Noy-Meir; Niles Eldredge; Cristiano Tabarroni; Ettore Randi

2008-01-01

280

Longitudinal patterns in species richness and genetic diversity in European oaks and oak gallwasps  

Microsoft Academic Search

While latitudinal patterns of genetic diversity are well known for many taxa in Europe, there has been little analysis of\\u000a longitudinal patterns across Pleistocene glacial refugia. Here we analyze longitudinal patterns in two aspects of diversity\\u000a (species richness and intraspecific genetic diversity) for two trophically related groups of organisms – oaks (Fagaceae, genus\\u000a Quercus) and their associated gallwasps (Hymenoptera: Cynipidae)

Rachel J. Atkinson; Antonis Rokas; Graham N. Stone

281

Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers  

Microsoft Academic Search

Molecular diversity in Saccharum complex was studied using 195 RAPD markers generated by 12 random primers. Among the Saccharum species, S. officinarum showed a low level of genetic diversity while S. sinense was found to be more diverse. Six taxonomical groups were clearly resolved in the cluster analysis. S. officinarum, S. robustum, S. spontaneum and Erianthus spp. formed discrete groups.

N. Vijayan Nair; Suresh Nair; T. V. Sreenivasan; Madan Mohan

1999-01-01

282

Genetic Diversity and Population Structure of Acacia senegal (L) Willd. in Kenya  

Microsoft Academic Search

The level of genetic diversity and population structure of Acacia senegal variety kerensis in Kenya was examined using seven polymorphic nuclear microsatellite loci and two chloroplast microsatellite loci. In both\\u000a chloroplast and nuclear datasets, high levels of genetic diversity were found within all populations and genetic differentiation\\u000a among populations was low, indicating extensive gene flow. Analysis of population structure provided

Stephen F. Omondi; Eliud Kireger; Otto G. Dangasuk; Ben Chikamai; David W. Odee; Stephen Cavers; Damase P. Khasa

2010-01-01

283

Discovering relationships in genetic regulatory networks  

E-print Network

The development of cDNA microarray technology has made it possible to simultaneously monitor the expression status of thousands of genes. A natural use for this vast amount of information would be to try and ?gure out inter-gene relationships...

Pal, Ranadip

2004-11-15

284

Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L.  

PubMed Central

Background Jatropha curcas L. has attracted a great deal of attention worldwide, regarding its potential as a new biodiesel crop. However, the understanding of this crop remains very limited and little genomic research has been done. We used simple sequence repeat (SSR) markers that could be transferred from Manihot esculenta (cassava) to analyze the genetic relationships among 45 accessions of J. curcas from our germplasm collection. Results In total, 187 out of 419 expressed sequence tag (EST)-SSR and 54 out of 182 genomic (G)-SSR markers from cassava were polymorphic among the J. curcas accessions. The EST-SSR markers comprised 26.20% dinucleotide repeats, 57.75% trinucleotide repeats, 7.49% tetranucleotide repeats, and 8.56% pentanucleotide repeats, whereas the majority of the G-SSR markers were dinucleotide repeats (62.96%). The 187 EST-SSRs resided in genes that are involved mainly in biological and metabolic processes. Thirty-six EST-SSRs and 20 G-SSRs were chosen to analyze the genetic diversity among 45 J. curcas accessions. A total of 183 polymorphic alleles were detected. On the basis of the distribution of these polymorphic alleles, the 45 accessions were classified into six groups, in which the genotype showed a correlation with geographic origin. The estimated mean genetic diversity index was 0.5572, which suggests that our J. curcas germplasm collection has a high level of genetic diversity. This should facilitate subsequent studies on genetic mapping and molecular breeding. Conclusion We identified 241 novel EST-SSR and G-SSR markers in J. curcas, which should be useful for genetic mapping and quantitative trait loci analysis of important agronomic traits. By using these markers, we found that the intergroup gene diversity of J. curcas was greater than the intragroup diversity, and that the domestication of the species probably occurred partly in America and partly in Hainan, China. PMID:20181259

2010-01-01

285

Highest genetic diversity at the northern range limit of the rare orchid Isotria medeoloides  

PubMed Central

Populations in previously glaciated regions are often genetically depauperate in comparison with populations at lower latitudes, due either to bottlenecks experienced in post-glacial colonization or to contemporary genetic drift in small, peripheral populations. Populations of the rare self-fertilizing North American orchid Isotria medeoloides are largest in the previously glaciated region near the northern range limit, allowing us to examine the role of historical versus contemporary processes in determining population genetic diversity and structure. If contemporary processes predominate, genetic diversity should increase with increasing census size. In contrast, if sequential bottlenecks associated with colonization are paramount, diversity should decrease with latitude and be relatively insensitive to census size. We genotyped 299 individuals from 20 populations at four variable microsatellite loci to contrast genetic diversity and structure for populations in previously glaciated regions versus previously unglaciated regions. Populations were highly inbred (F=0.95) and highly differentiated (RST=0.485). Across all sampled populations, genetic diversity decreased and genetic differentiation increased with declining population size. Small southern populations were especially differentiated and genetically depauperate. In the glaciated part of the range, genetic diversity increased as populations approached the northern range limit, demonstrating the centrality of contemporary processes for this post-glacial colonist. PMID:22692268

Stone, J L; Crystal, P A; Devlin, E E; Downer, R H LeB; Cameron, D S

2012-01-01

286

Conservation of genetic diversity in the endangered plant Eriogonum ovalifolium var. vineum (Polygonaceae)  

Microsoft Academic Search

The purpose of his research was to describethe organization of genetic variation in thefederally endangered plant taxon Eriogonumovalifolium var. vineum using allozymes. Such information can help prioritize sites andmanagement choices for capturing andmaintaining genetic variation and can reducethe number of populations necessary to committo conservation, thus reducing costs andconflicts with competing land uses. Information on genetic diversity patterns alsoprovides insight

Maile C. Neel; Norman C. Ellstrand

2003-01-01

287

Genetic relationships within the genus Prevotella analyzed by multilocus enzyme electrophoresis and DNA-DNA hybridization.  

PubMed

The genetic diversity and relationships within the genus Prevotella were studied by analyzing twenty-five strains by multilocus enzyme electrophoresis (MLEE) at nine metabolic enzyme loci and DNA-DNA hybridization. MLEE revealed a high genetic diversity with 25 electrophoretic types (ETs) for the 25 strains studied, a mean number of alleles per enzyme locus of 6.8 and a mean genetic diversity per locus of 0.786. The index of association described by Maynard Smith et al. (1993) revealed a clonal structure within the genus Prevotella. A dendrogram generated by cluster analysis of a matrix of ETs showed that species like P. bivia, P. buccae, P. oris, P. oralis, P. nigrescens, and P. denticola form clusters that are consistent with DNA homologies. However, strains identified as P. melaninogenica or P. loescheii by DNA-DNA hybridization did not constitute distinct subpopulations in MLEE. MLEE analysis demonstrated its high power in differentiating closely related strains. It provides an alternative to 16S rRNA analysis for the study of phylogenetic relationships within the genus Prevotella, especially for differentiating strains with high DNA homology or high rRNA homology. PMID:10794148

Combe, M L; Pons, J L

1999-12-01

288

Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity  

PubMed Central

The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second–nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth–nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis. PMID:24573854

Muller, Romy; Roberts, Charlotte A.; Brown, Terence A.

2014-01-01

289

Prevalence and genetic diversity of bovine kobuvirus in China.  

PubMed

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

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

2014-06-01

290

Occurrence and genetic diversity of pigeon circovirus strains in Poland.  

PubMed

Pigeon circovirus (PiCV) is an immunosuppressive agent widespread throughout the world, which causes a disease in pigeons called Young Pigeon Disease Syndrome. The aim of the study was to evaluate the prevalence of PiCV in Poland and investigate the genetic diversity relative to other known PiCV isolates. Samples from 152 pigeon flocks (88 flocks of racing pigeons and 64 flocks of fancy pigeons) from various regions of Poland were tested by polymerase chain reaction and an approximately 326-base fragment of the capsid protein gene (Cap gene) of the virus was amplified. The average viral prevalence was found to be 70.3% (76.13% in racing pigeons and 62.5% in fancy pigeons). Among the obtained positive samples, 21 were selected for sequencing and a phylogenetic analysis was performed. It was found that the majority of Polish PiCV isolates, to varying degrees, are related to isolates occurring in Europe. It was also observed that the Cap gene is variable and mutations often occur in it, which impacts the amino acid sequences in the capsid protein (nucleotide similarity averaged 86.57%, amino acid similarity averaged 89.02%). PMID:24659711

Stenzel, Tomasz; Pestka, Daria

2014-06-01

291

Genetic diversity of feline morbilliviruses isolated in Japan.  

PubMed

Feline morbillivirus (FmoPV) is an emerging virus in domestic cats and considered to be associated with tubulointerstitial nephritis. Although FmoPV was first described in China in 2012, there has been no report of the isolation of this virus in other countries. In this report, we describe the isolation and characterization of FmoPV from domestic cats in Japan. By using reverse transcription (RT)-PCR, we found that three of 13 urine samples from cats brought to veterinary hospitals were positive for FmoPV. FmoPV strains SS1 to SS3 were isolated from the RT-PCR-positive urine samples. Crandell-Rees feline kidney (CRFK) cells exposed to FmoPV showed cytopathic effects with syncytia formation, and FmoPV N protein was detected by indirect immunofluorescence assays. In addition, pleomorphic virus particles with apparent glycoprotein envelope spikes were observed by electron microscopy. By sequence analysis of FmoPV H and L genes, we found that FmoPVs showed genetic diversity; however, signatures of positive selection were not identified. PMID:24728711

Sakaguchi, Shoichi; Nakagawa, So; Yoshikawa, Rokusuke; Kuwahara, Chieko; Hagiwara, Hiroko; Asai, Ken-ichi; Kawakami, Kazuo; Yamamoto, Yu; Ogawa, Makoto; Miyazawa, Takayuki

2014-07-01

292

Genetic Diversity among Xanthomonas campestris Strains Pathogenic for Small Grains  

PubMed Central

A collection of 51 Xanthomonas campestris strains from throughout the world was studied to detect and assess genetic diversity among pathogens of small grains. Isolates from barley, bread wheat, bromegrass, canary grass, cassava, maize, orchard grass, rice, rough-stalked meadow grass, rye, timothy, and triticale were analyzed by pathogenicity tests on bread wheat cv. Alondra and barley cv. Corona, indirect immunofluorescence, and restriction fragment length polymorphism (RFLP). Three probes were used for the RFLP analysis. They were an acetylaminofluorene-labelled 16S+23S rRNA probe from Escherichia coli and two (sup32)P-labelled restriction fragments from either plasmidic (pBSF2) or chromosomal (pBS8) DNA of X. campestris pv. manihotis. Strains clustered in 9 and 20 groups with the rRNA probe and the pBSF2 DNA probe, respectively. Strains of X. campestris pv. graminis, X. campestris pv. phleipratensis, and X. campestris pv. poae are shown to be related but are also distinguishable by RFLP patterns, serology, and pathogenicity on bread wheat. Strains pathogenic only for barley and not for wheat grouped together. Another group is temporarily designated deviant X. campestris pv. undulosa. These South American isolates from bread wheat did not react by indirect immunofluorescence and produced atypical lesions in pathogenicity tests. The results stress the need to perform pathogenicity tests before strains are named at the pathovar level. The importance of the different probes used for epidemiological studies or phylogenetic studies of closely related strains is underlined. PMID:16534952

Bragard, C.; Verdier, V.; Maraite, H.

1995-01-01

293

Delineating genetic relationships among the Maya.  

PubMed

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

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

2008-03-01

294

Prediction of progeny variation in oat from parental genetic relationships  

Microsoft Academic Search

The ability to predict agronomic performance of progeny from a cross would be a great benefit to plant breeders in selecting parents. The predictive value of parental genetic relationships estimating F1 progeny means and F4 family variances of nine argronomic traits was tested in 76 oat crosses, using genetic distance measures based on coefficients-of-parentage, quantitatively inherited morphological characters, and discretely

E. Souza; M. E. Sorrells

1991-01-01

295

Use of EST-SSR markers for evaluating genetic diversity and fingerprinting celery (Apium graveolens L.) cultivars.  

PubMed

Celery (Apium graveolens L.) is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting celery molecular breeding are quite limited, thus few studies on celery have been conducted so far. In this study we made use of simple sequence repeat (SSR) markers generated from previous celery transcriptome sequencing and attempted to detect the genetic diversity and relationships of commonly used celery accessions and explore the efficiency of the primers used for cultivars identification. Analysis of molecular variance (AMOVA) of Apium graveolens L. var. dulce showed that approximately 43% of genetic diversity was within accessions, 45% among accessions, and 22% among horticultural types. The neighbor-joining tree generated by unweighted pair group method with arithmetic mean (UPGMA), and population structure analysis, as well as principal components analysis (PCA), separated the cultivars into clusters corresponding to the geographical areas where they originated. Genetic distance analysis suggested that genetic variation within Apium graveolens was quite limited. Genotypic diversity showed any combinations of 55 genic SSRs were able to distinguish the genotypes of all 30 accessions. PMID:24518809

Fu, Nan; Wang, Ping-Yong; Liu, Xiao-Dan; Shen, Huo-Lin

2014-01-01

296

Centres of Crop Diversity and\\/or Origin, Genetically Modified Crops and Implications for Plant Genetic Resources Conservation  

Microsoft Academic Search

The concept of centres of crop diversity and\\/or origin of agriculture is briefly reviewed. The conservation status of crop genetic resources, either ex situ or in situ, cultivated or wild, has been assessed for species of the Central American and Mexican centre, demonstrating that that region is indeed one of the important centres of crop diversity for human kind. Furthermore,

J. M. M. Engels; A. W. Ebert; I. Thormann; M. C. de Vicente

2006-01-01

297

Landscape models for nuclear genetic diversity and genetic structure in white-footed mice (Peromyscus leucopus).  

PubMed

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

Taylor, Z S; Hoffman, S M G

2014-06-01

298

Inferring population structure and genetic diversity of broad range of wild diploid alfalfa (Medicago sativa L.) accessions using SSR markers.  

PubMed

Diversity analyses in alfalfa have mainly evaluated genetic relationships of cultivated germplasm, with little known about variation in diploid germplasm in the M. sativa-falcata complex. A collection of 374 individual genotypes derived from 120 unimproved diploid accessions from the National Plant Germplasm System, including M. sativa subsp. caerulea, falcata, and hemicycla, were evaluated with 89 polymorphic SSR loci in order to estimate genetic diversity, infer the genetic bases of current morphology-based taxonomy, and determine population structure. Diploid alfalfa is highly variable. A model-based clustering analysis of the genomic data identified two clearly discrete subpopulations, corresponding to the morphologically defined subspecies falcata and caerulea, with evidence of the hybrid nature of the subspecies hemicycla based on genome composition. Two distinct subpopulations exist within each subsp. caerulea and subsp. falcata. The distinction of caerulea was based on geographical distribution. The two falcata groups were separated based on ecogeography. The results show that taxonomic relationships based on morphology are reflected in the genetic marker data with some exceptions, and that clear distinctions among subspecies are evident at the diploid level. This research provides a baseline from which to systematically evaluate variability in tetraploid alfalfa and serves as a starting point for exploring diploid alfalfa for genetic and breeding experiments. PMID:20352180

Sakiro?lu, Muhammet; Doyle, Jeffrey J; Charles Brummer, E

2010-08-01

299

Using Disruptive Selection to Maintain Diversity in Genetic Algorithms  

Microsoft Academic Search

Genetic algorithms are a class of adaptive search techniques based on the principles of population genetics. The metaphor underlying genetic algorithms is that of natural evolution. With their great robustness, genetic algorithms have proven to be a promising technique for many optimization, design, control, and machine learning applications. A novel selection method, disruptive selection, has been proposed. This method adopts

Ting Kuo; Shu-Yuen Hwang

1997-01-01

300

[Genetic variation and relationship in orchardgrass (Dactylis glomerata L.) germplasm detected by SSR markers].  

PubMed

Genetic variation and relationship of 53 accessions of D. glomerata collected from 5 continents were analyzed using simple sequence repeat (SSR) molecular markers with 15 SSR primer pairs. The following results were obtained. (1) A total of 127 alleles were detected at 15 loci. The number of alleles per locus ranged from 5 to 12, with an average of 8.5. The rate of polymorphic sites (P) was 95.21%; the polymorphic information content (PIC) ranged from 0.30(A04C24)to 0.44(A01F24) with an average of 0.36. (2) The genetic similarity (GS) among all accessions ranged from 0.43 to 0.94, for all geographical groups GS ranged from 0.73 to 0.91, and high genetic diversity was observed in Asia (P, 90.55%) and Europe (P, 86.61%) groups. These results suggested that there was rich genetic diversity among all orchardgrass accessions tested. (3) Based on the cluster and principal component analyses, 53 accessions could be divided into five groups according to the nearest phylogenetic relationship, and accessions from the same continent were classified into the same group associated with their geographical distributions. PMID:19586867

Xie, Wen-Gang; Zhang, Xin-Quan; Ma, Xiao; Peng, Yan; Huang, Lin-Kai

2009-06-01

301

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

PubMed

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

Gillis, Annika; Mahillon, Jacques

2014-07-01

302

Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry  

PubMed Central

Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues. PMID:20691402

McEvoy, Brian P.; Lind, Joanne M.; Wang, Eric T.; Moyzis, Robert K.; Visscher, Peter M.; van Holst Pellekaan, Sheila M.; Wilton, Alan N.

2010-01-01

303

Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape  

USGS Publications Warehouse

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.

Mushet, David M.; Euliss, Ned H., Jr.; Chen, Yongjiu; Stockwell, Craig A.

2013-01-01

304

Genetic diversity of Guernsey population using pedigree data and gene-dropping simulations.  

PubMed

The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS. PMID:23032118

Melka, M G; Sargolzaei, M; Miglior, F; Schenkel, F

2013-02-01

305

Social Category Diversity Promotes Premeeting Elaboration: The Role of Relationship Focus  

E-print Network

A purported downside of social category diversity is decreased relationship focus (i.e., one’s focus on establishing a positive social bond with a coworker). However, we argue that this lack of relationship focus serves ...

Loyd, Denise Lewin

306

[Research progress on molecular genetic diversity of the yak (Bos grunniens)].  

PubMed

Studies on genetic diversity, as the core of population genetics, reveal genetic variations of the yak (Bos grunniens). Since the 1970s, the morphological, chromosomal, physiological, and biochemical characteristics, as well as DNA sequence polymorphisms, in yak have been extensively investigated. Following the rapid development of molecular genetics and DNA sequencing technology, the molecular genetic diversity of yak has become a focus in recent studies. In this paper, the research progress on the molecular genetic diversity of yak was reviewed based on the information and knowledge on mtDNA sequences and nucleus molecular markers, as well as candidate genes, obtained over the last 15 years. The future perspectives of relevant research topics were discussed to shed more light on depth understanding of the population genomics of the yak. PMID:23448927

Ma, Zhi-Jie; Zhong, Jin-Cheng; Han, Jian-Lin; Xu, Jing-Tao; Liu, Zhong-Na; Bai, Wen-Lin

2013-02-01

307

Genetic Diversity Among Monoconidial and Polyconidial Isolates of Bipolaris sorokiniana.  

PubMed

Spot blotch caused by Bipolaris sorokiniana is a destructive disease of wheat in warm and humid wheat-growing regions of the world. This fungus shows a high genetic diversity and morphological and physiologic variability. In this study, 19 polysporic and 57 monosporic isolates of B. sorokiniana were characterized using universal rice primers-URP-PCR. The results obtained when the dendrogram was constructed with all the data produced with the amplification products showed very distinct clusters. However, the similarity among the isolates was low where 37 and 26.3 % of the monosporic and polysporic isolates, respectively, showed similarity above 70 %. All primers amplified multiple DNA fragments of polysporic as well as the monosporic isolates. Isolates fingerprints were constructed based on binary characters revealed by the three primers. An amplified fragment of approximately 750 bp was observed among 40 % of the isolates, when primer URP-1F was used. When primers URP-4R and URP-2R were used, a fragment of 450 and 400 bp was present in 31.5 and 29 % of the isolates, respectively. It was expected a higher similarity among the isolates since the monosporic cultures were originated from the polysporic. The dendrogram did not enable the separation of B. sorokiniana isolates by their geographic origin. This low correlation suggests that gene transfer may have occurred by parasexual combination in this fungus population. However, in spite of the research efforts for that end, it has not been possible to establish patterns that characterize the profile of B. sorokiniana. PMID:25100225

Mann, Michele B; Minotto, Elisandra; Feltrin, Thaisa; Milagre, Luciana P; Spadari, Cristina; Van Der Sand, Sueli T

2014-12-01

308

Molecular biology and genetic diversity of Rift Valley fever virus  

PubMed Central

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

Ikegami, Tetsuro

2013-01-01

309

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

PubMed

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

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

2012-03-01

310

Genetic diversity of root nodule bacteria nodulating Lotus corniculatus and Anthyllis vulneraria in Sweden.  

PubMed

Very little is known about the genetic diversity and phylogeny of rhizobia nodulating Lotus species in northern temperate regions. We have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from Lotus corniculatus and Anthyllis vulneraria from different geographic sites and habitats in Sweden by restriction fragment length polymorphism (RFLP) of the internal transcribed spacer between their 16S rRNA and 23S rRNA (IGS) region. A high diversity consisting of 26 IGS types from 54 L. corniculatus isolates and five IGS types from seven A. vulneraria isolates was found. The 16S rRNA sequences and phylogeny of representatives of the different IGS types showed four interesting exceptions from the majority of the isolates belonging to the genus Mesorhizobium: Two isolates were both found to be closely related to Rhodococcus spp., and two other isolates showed close relationship with Geobacillus spp. and Paenibacillus spp., respectively. The nodA sequences and phylogeny showed that all the isolates, including those not belonging to the traditional rhizobia genera, harbored nodA sequences which were typical of Mesorhizobium loti. Generally, the 16S rRNA and nodA phylogenetic trees were not congruent in that isolates with similar 16S rRNA sequences were associated with isolates harboring different nodA sequences. All the isolates were confirmed to nodulate L. corniculatus in an inoculation test. This is the first report of members of these non-rhizobia genera being able to nodulate legumes, and we suggest that they may have acquired their nodulating properties through lateral gene transfer. PMID:21497473

Ampomah, Osei Yaw; Huss-Danell, Kerstin

2011-06-01

311

ORIGINAL ARTICLE The relationship between parental genetic or phenotypic  

E-print Network

ORIGINAL ARTICLE The relationship between parental genetic or phenotypic divergence and progeny,4,5, S Flint-Garcia2,6, MD McMullen2,6, TR Rocheford3,7 and JB Holland1,2 Appropriate selection of parents studies. Accurate prediction of the most useful parental combinations within a species would help guide

Flint-Garcia, Sherry

312

Genetic Relationship between Cocirculating Human Enteroviruses Species C  

E-print Network

Genetic Relationship between Cocirculating Human Enteroviruses Species C Mae¨l Bessaud1 Recombination events between human enteroviruses (HEV) are known to occur frequently and to participate to the Human enterovirus species C (HEV-C) that had been cocirculating in a small geographic area of Madagascar

Paris-Sud XI, Université de

313

Elucidating the temporal and spatial dynamics of Biomphalaria glabrata genetic diversity in three Brazilian villages  

PubMed Central

Objective The freshwater snail Biomphalaria glabrata is the principal intermediate host for the parasite Schistosoma mansoni within Brazil. We assessed the potential effects of snail population dynamics on parasite transmission dynamics via population genetics. Methods We sampled snail populations located within the confines of three schistosome-endemic villages in the state of Minas Gerais, Brazil. Snails were collected from individual microhabitats following seasonal periods of flood and drought over the span of one year. Snail spatio-temporal genetic diversity and population differentiation of 598 snails from 12 sites were assessed at 7 microsatellite loci. Results Average genetic diversity was relatively low, ranging from 4.29 to 9.43 alleles per locus and, overall, subpopulations tended to exhibit heterozygote deficits. Genetic diversity was highly spatially partitioned among subpopulations, while virtually no partitioning was observed across temporal sampling. Comparison with previously published parasite genetic diversity data indicated that S. mansoni populations are significantly more variable and less subdivided than those of the B. glabrata intermediate hosts. Discussion Within individual Brazilian villages, observed distributions of snail genetic diversity indicate temporal stability and very restricted gene flow. This is contrary to observations of schistosome genetic diversity over the same spatial scale, corroborating the expectation that parasite gene flow at the level of individual villages is likely driven by vertebrate host movement. PMID:23911082

Thiele, Elizabeth A.; Correa-Oliveira, Guilherme; Gazzinelli, Andrea; Minchella, Dennis J.

2013-01-01

314

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

PubMed Central

Background The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. Results The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. Conclusions The results reported improve our understanding of the combined effects of geography, ecology and human intervention on organization of the C. baccatum genepool. The results will facilitate utilization of C. baccatum for crop improvement and species conservation by providing a framework for efficient germplasm collection management and guidance for future plant acquisitions. PMID:22866868

2012-01-01

315

Peak and Persistent Excess of Genetic Diversity Following an Abrupt Migration Increase  

PubMed Central

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species’ lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population’s demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations. PMID:23307901

Alcala, Nicolas; Streit, Daniela; Goudet, Jérôme; Vuilleumier, Séverine

2013-01-01

316

Genetic diversity in caribou linked to past and future climate change  

NASA Astrophysics Data System (ADS)

Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species' evolutionary potential. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.

Yannic, Glenn; Pellissier, Loïc; Ortego, Joaquín; Lecomte, Nicolas; Couturier, Serge; Cuyler, Christine; Dussault, Christian; Hundertmark, Kris J.; Irvine, R. Justin; Jenkins, Deborah A.; Kolpashikov, Leonid; Mager, Karen; Musiani, Marco; Parker, Katherine L.; Røed, Knut H.; Sipko, Taras; Þórisson, Skarphéðinn G.; Weckworth, Byron V.; Guisan, Antoine; Bernatchez, Louis; Côté, Steeve D.

2014-02-01

317

Peak and persistent excess of genetic diversity following an abrupt migration increase.  

PubMed

Genetic diversity is essential for population survival and adaptation to changing environments. Demographic processes (e.g., bottleneck and expansion) and spatial structure (e.g., migration, number, and size of populations) are known to shape the patterns of the genetic diversity of populations. However, the impact of temporal changes in migration on genetic diversity has seldom been considered, although such events might be the norm. Indeed, during the millions of years of a species' lifetime, repeated isolation and reconnection of populations occur. Geological and climatic events alternately isolate and reconnect habitats. We analytically document the dynamics of genetic diversity after an abrupt change in migration given the mutation rate and the number and sizes of the populations. We demonstrate that during transient dynamics, genetic diversity can reach unexpectedly high values that can be maintained over thousands of generations. We discuss the consequences of such processes for the evolution of species based on standing genetic variation and how they can affect the reconstruction of a population's demographic and evolutionary history from genetic data. Our results also provide guidelines for the use of genetic data for the conservation of natural populations. PMID:23307901

Alcala, Nicolas; Streit, Daniela; Goudet, Jérôme; Vuilleumier, Séverine

2013-03-01

318

SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors  

PubMed Central

Background Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. Results In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. Conclusions Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors. PMID:23937410

2013-01-01

319

Prevalent Ciliate Symbiosis on Copepods: High Genetic Diversity and Wide Distribution Detected Using Small Subunit Ribosomal RNA Gene  

PubMed Central

Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA)-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups), six (containing 99% of all the sequences) belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus), and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally. PMID:23024768

Guo, Zhiling; Liu, Sheng; Hu, Simin; Li, Tao; Huang, Yousong; Liu, Guangxing; Zhang, Huan; Lin, Senjie

2012-01-01

320

Soil fungal pathogens and the relationship between plant diversity and productivity  

E-print Network

LETTER Soil fungal pathogens and the relationship between plant diversity and productivity John L whether suppression of plant productivity by soil fungal pathogens might also drive a positive diversity treatment. In control (non-fungicide treated) assemblages there was a strong positive relationship between

Cleveland, Cory

321

Tetraploid Wheat Landraces in the Mediterranean Basin: Taxonomy, Evolution and Genetic Diversity  

PubMed Central

The geographic distribution of genetic diversity and the population structure of tetraploid wheat landraces in the Mediterranean basin has received relatively little attention. This is complicated by the lack of consensus concerning the taxonomy of tetraploid wheats and by unresolved questions regarding the domestication and spread of naked wheats. These knowledge gaps hinder crop diversity conservation efforts and plant breeding programmes. We investigated genetic diversity and population structure in tetraploid wheats (wild emmer, emmer, rivet and durum) using nuclear and chloroplast simple sequence repeats, functional variations and insertion site-based polymorphisms. Emmer and wild emmer constitute a genetically distinct population from durum and rivet, the latter seeming to share a common gene pool. Our population structure and genetic diversity data suggest a dynamic history of introduction and extinction of genotypes in the Mediterranean fields. PMID:22615891

Oliveira, Hugo R.; Campana, Michael G.; Jones, Huw; Hunt, Harriet V.; Leigh, Fiona; Redhouse, David I.; Lister, Diane L.; Jones, Martin K.

2012-01-01

322

On indigenous production, genetic diversity and crop ecology of enset (Ensete ventricosum (Welw.) Cheesman)  

Microsoft Academic Search

Keywords<\\/strong> : Enset, staple, indigenous knowledge, genetic diversity, AFLP, characterisation, conservation, Leaf Appearance Rate, Radiation Use Efficiency, yield potential, transplanting, leaf pruning, fermentation, 'kocho', food security

A. Tsegaye

2002-01-01

323

GENETIC DIVERSITY, POPULATION SUBDIVISION AND GENE FLOW IN MORELET'S CROCODILE (CROCODYLUS MORELETII) FROM BELIZE, CENTRAL  

E-print Network

1 Title: GENETIC DIVERSITY, POPULATION SUBDIVISION AND GENE FLOW IN MORELET'S CROCODILE (CROCODYLUS, microsatellites, conservation Suggested Running Head: Gene flow in Morelet's crocodile populations Manuscript surrounding natural history and ecology of the endangered Morelet's crocodile (Crocodylus moreletii) has

Dever, Jennifer A.

324

Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida  

E-print Network

Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic distributed insect host, the oak gallwasp Biorhiza pallida (Hymenoptera: Cynipidae). Two hundred and eighteen a Wolbachia-associated selective sweep. Keywords: cytochrome b, gallwasp, phylogeography, range expansion

West, Stuart

325

Genetic diversity and performance of maize varieties from Zimbabwe, Zambia and Malawi  

E-print Network

studies were conducted to generate information on the current levels of genetic diversity and agronomic performance of both farmer-developed and commercially-bred maize varieties in Zimbabwe, Zambia and Malawi to help in the identification of sources...

Magorokosho, Cosmos

2007-04-25

326

High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis.  

PubMed

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to its widespread congener, Boechera stricta, which shares similar life history and mating system. Despite its rarity, B. fecunda had levels of genetic diversity similar to B. stricta for both microsatellites and nucleotide polymorphism. Populations of B. fecunda are highly differentiated, with a majority of genetic diversity existing among populations (F(ST) = 0.57). Differences in molecular diversity and allele frequencies between western and eastern population groups suggest they experienced very different evolutionary histories. PMID:17784916

Song, Bao-Hua; Mitchell-Olds, Thomas

2007-10-01

327

Genetic diversity in two introduced biofouling amphipods (Amphipods valida and Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity  

EPA Science Inventory

We investigated patterns of genetic diversity among invasive populations of A. valida and J. marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute...

328

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

PubMed Central

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

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

1998-01-01

329

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

USGS Publications Warehouse

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations. ?? 2010 US Government.

Huff, D.D.; Miller, L.M.; Vondracek, B.

2010-01-01

330

Global diversity and genetic contributions of chicken populations from African, Asian and European regions.  

PubMed

Genetic diversity and population structure of 113 chicken populations from Africa, Asia and Europe were studied using 29 microsatellite markers. Among these, three populations of wild chickens and nine commercial purebreds were used as reference populations for comparison. Compared to commercial lines and chickens sampled from the European region, high mean numbers of alleles and a high degree of heterozygosity were found in Asian and African chickens as well as in Red Junglefowl. Population differentiation (FST ) was higher among European breeds and commercial lines than among African, Asian and Red Junglefowl populations. Neighbour-Net genetic clustering and structure analysis revealed two main groups of Asian and north-west European breeds, whereas African populations overlap with other breeds from Eastern Europe and the Mediterranean region. Broilers and brown egg layers were situated between the Asian and north-west European clusters. structure analysis confirmed a lower degree of population stratification in African and Asian chickens than in European breeds. High genetic differentiation and low genetic contributions to global diversity have been observed for single European breeds. Populations with low genetic variability have also shown a low genetic contribution to a core set of diversity in attaining maximum genetic variation present from the total populations. This may indicate that conservation measures in Europe should pay special attention to preserving as many single chicken breeds as possible to maintain maximum genetic diversity given that higher genetic variations come from differentiation between breeds. PMID:25315897

Lyimo, C M; Weigend, A; Msoffe, P L; Eding, H; Simianer, H; Weigend, S

2014-12-01

331

Genetic connections among Turkic-speaking Iranian ethnic groups based on HLA class II gene diversity.  

PubMed

Iran is a linguistically heterogeneous nation where Persian, Turkic and Arabic are the three main language families spoken. Based on their linguistic properties, Qashqais, Turkmens and Azeris are Turkic-speaking people. The purpose of this study was to investigate whether any genetic relationship exists among the Turkic-speaking Iranian subpopulations based on HLA class II gene diversity. HLA-DRB1, DQA1 and DQB1 alleles were identified by PCR-based methods in 100 Qashqais and 66 Turkmens, and the results were compared with our previously published HLA data for Azeris. Despite a number of allelic and haplotypic similarities, Qashqais, Turkmens and Azeris were not in the same clade of the phylogenetic tree. However, based on the results of principal coordinates analysis, they are grouped together with Kurds and Bakhtiaris. Contrary to their common linguistic features, the Turkic-speaking people of Iran are closer to other Iranian subpopulations than to the people of Turkey and central Asia. Overall, it seems that linguistic criteria alone are not able to determine the relationships among these populations, and a combination of different kinds of anthropological information should be used to determine their actual phylogenetic relationships. PMID:23745951

Farjadian, S; Safi, S

2013-12-01

332

Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing.  

PubMed

Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis. PMID:24814796

Crauwels, Sam; Zhu, Bo; Steensels, Jan; Busschaert, Pieter; De Samblanx, Gorik; Marchal, Kathleen; Willems, Kris A; Verstrepen, Kevin J; Lievens, Bart

2014-07-01

333

Allozyme diversity and genetic structure of European populations of Sorbus aucuparia L. (Rosaceae: Maloideae)  

Microsoft Academic Search

Genetic diversity at 10 loci encoding six enzymes was studied in 17 European populations of Sorbus aucuparia L. (the rowan), distributed among five regions, from Finland to the Pyrenees. Levels of genetic diversity were high both at the species level (He=0.229) and within populations (mean He=0.212), whereas levels of differentiation among populations were very low (GST=0.060). These values were comparable

Olivier Raspé; Anne-Laure Jacquemart

1998-01-01

334

The structure of population genetic diversity in Vallisneria americana in the Chesapeake Bay: implications for restoration  

Microsoft Academic Search

Submersed aquatic macrophyte beds provide important ecosystem services, yet their distribution and extent has declined worldwide\\u000a in aquatic ecosystems. Effective restoration of these habitats will require, among other factors, reintroduction of genetically\\u000a diverse source material that can withstand short- and long-term environmental fluctuations in environmental conditions. We\\u000a examined patterns of genetic diversity in Vallisneria\\u000a americana because it is a cosmopolitan

Michael W. LloydRobert; Robert K. Burnett; Katharina A. M. Engelhardt; Maile C. Neel

335

Genetic diversity in the threatened insular endemic plant Aster asa-grayi ( Asteraceae )  

Microsoft Academic Search

Genetic diversity in an insular endemic plantAster asa-grayi was examined using enzyme electrophoresis. Distribution ofA. asa-grayi is restricted to only four subtropical islands of Japan, and this species is listed as ‘vulnerable to extinction’ in the Red Data Book of Japanese wild plants. A total of 161 individuals were sampled from five populations on four islands. Genetic diversity values at

Masayuki Maki

1999-01-01

336

Frankia bacteria in Alnus rubra forests: genetic diversity and determinants of assemblage structure  

Microsoft Academic Search

To quantify the genetic diversity of Frankia bacteria associated with Alnus rubra in natural settings and to examine the relative importance of site age, management, and geographic location in structuring\\u000a Frankia assemblages in A. rubra forests, root nodules from four A. rubra sites in the Pacific Northwest, USA were sampled. Frankia genetic diversity at each site was compared using sequence-based

Peter G. Kennedy; Marjorie G. Weber; Andrew A. Bluhm

2010-01-01

337

Genetic diversity of Poa annua in western Oregon grass seed crops  

Microsoft Academic Search

The genetic diversity of Poa annua L.populations collected from western Oregon grass-seed fields was surveyed using 18 randomly amplified polymorphic DNA (RAPD) markers. Markers from 1357 individual plants from 47 populations collected at three sampling dates (fall, winter, and\\u000a spring) for 16 sites were used to measure genetic diversity within and among populations. Site histories varied from low to\\u000a high

L. W. Mengistu; G. W. Mueller-Warrant; R. E. Barker

2000-01-01

338

Genome-wide characterization of genetic diversity and population structure in Secale  

PubMed Central

Background Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. Results Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. Conclusions Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies. PMID:25085433

2014-01-01

339

Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs.  

PubMed

The recent availability of a genome-wide SNP array for the goat genome dramatically increases the power to investigate aspects of genetic diversity and to conduct genome-wide association studies in this important domestic species. We collected and analysed genotypes from 52 088 SNPs in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Principal components analysis revealed a clear genetic division between animals for each population, and model-based clustering successfully detected evidence of admixture that matched aspects of their recorded history. For example, shared co-ancestry was detected, suggesting Boer goats have been introgressed into the Rangeland population. Further, allele frequency data successfully tracked the altered genetic profile that has taken place after 40 years of breeding Australian Cashmere goats using the Rangeland animals as the founding population. Genome-wide association mapping of the POLL locus revealed a strong signal on goat chromosome 1. The 769-kb critical interval contained the polled intersex syndrome locus, confirming the genetic basis in non-European animals is the same as identified previously in Saanen goats. Interestingly, analysis of the haplotypes carried by a small set of sex-reversed animals, known to be associated with polledness, revealed some animals carried the wild-type chromosome associated with the presence of horns. This suggests a more complex basis for the relationship between polledness and the intersex condition than initially thought while validating the application of the goat SNP50 BeadChip for fine-mapping traits in goat. PMID:23216229

Kijas, James W; Ortiz, Judit S; McCulloch, Russell; James, Andrew; Brice, Blair; Swain, Ben; Tosser-Klopp, Gwenola

2013-06-01

340

The effects of riverine physical complexity on anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss around the Pacific Rim.  

PubMed

This study explored the relationship between riverine physical complexity, as determined from remotely sensed metrics, and anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss. The proportion of anadromy (estimated fraction of individuals within a drainage that are anadromous) was correlated with riverine complexity, but this correlation appeared to be driven largely by a confounding negative relationship between drainage area and the proportion of anadromy. Genetic diversity decreased with latitude, was lower in rivers with only non-anadromous individuals and also decreased with an increasing ratio of floodplain area to total drainage area. Anadromy may be less frequent in larger drainages due to the higher cost of migration associated with reaches farther from the ocean, and the negative relationship between genetic diversity and floodplain area may be due to lower effective population size resulting from greater population fluctuations associated with higher rates of habitat turnover. Ultimately, the relationships between riverine physical complexity and migratory life history or genetic diversity probably depend on the spatial scale of analysis. PMID:24766581

McPhee, M V; Whited, D C; Kuzishchin, K V; Stanford, J A

2014-07-01

341

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

PubMed

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

Porlier, Mélody; Bélisle, Marc; Garant, Dany

2009-06-12

342

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

PubMed Central

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

Porlier, Melody; Belisle, Marc; Garant, Dany

2009-01-01

343

Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal  

Microsoft Academic Search

To date Borrelia lusitaniae is the only genospecies of Borrelia burgdorferi sensu lato isolated from Ixodes ricinus ticks collected in Portugal and Tunisia. This suggests that the genospecies diversity of B. burgdorferi sensu lato decreases toward the southwestern margin of its Old World subtropical range. In order to further explore the genetic diversity of B. burgdorferi sensu lato from this

SIMONA DE MICHELIS; HENNA-SISKO SEWELL; MARGARIDA COLLARES-PEREIRA; MARGARIDA SANTOS-REIS; LEO M. SCHOULS; VLADIMIR BENES; EDWARD C. HOLMES; KLAUS KURTENBACH

2000-01-01

344

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

Microsoft Academic Search

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 (Hes 5 0.66)

O. V. Tsyusko; MICHAEL H. SMITH; R EBECCA R. SHARITZ; TRAVIS C. GLENN

2005-01-01

345

Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata  

Microsoft Academic Search

The reconstruction of recent historical population sizes allowed us to investigate the influence of random evolutionary processes on present-day genetic diversity in populations of Dryopteris cristata. This long-lived, allotetraploid fern is rare and endangered in the study area at the southwestern border of its European distribution. Random amplified polymorphic DNA (RAPD) diversity of 280 individuals from 14 populations of D.

Urs Landergott; Rolf Holderegger; Gregor Kozlowski; J Jakob Schneller

2001-01-01

346

Assessment of genetic diversity in broomcorn millet ( Panicum miliaceum L.) using SSR markers  

Microsoft Academic Search

The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, wasanalyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles werefound, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91.

Xingyu Hu; Jianfei Wang; Ping Lu; Hongsheng Zhang

2009-01-01

347

Genetic and developmental basis of cichlid trophic diversity  

Microsoft Academic Search

Cichlids have undergone extensive evolutionary modifications of their feeding apparatus, making them an ideal model to study the factors that underlie craniofacial diversity. Recent studies have provided critical insights into the molecular mechanisms that have contributed to the origin and maintenance of cichlid trophic diversity. We review this body of work, which shows that the cichlid jaw is regulated by

R C Albertson; T D Kocher

2006-01-01

348

Host-plant genotypic diversity and community genetic interactions mediate aphid spatial distribution  

PubMed Central

Genetic variation in plants can influence the community structure of associated species, through both direct and indirect interactions. Herbivorous insects are known to feed on a restricted range of plants, and herbivore preference and performance can vary among host plants within a species due to genetically based traits of the plant (e.g., defensive compounds). In a natural system, we expect to find genetic variation within both plant and herbivore communities and we expect this variation to influence species interactions. Using a three-species plant-aphid model system, we investigated the effect of genetic diversity on genetic interactions among the community members. Our system involved a host plant (Hordeum vulgare) that was shared by an aphid (Sitobion avenae) and a hemi-parasitic plant (Rhinanthus minor). We showed that aphids cluster more tightly in a genetically diverse host-plant community than in a genetic monoculture, with host-plant genetic diversity explaining up to 24% of the variation in aphid distribution. This is driven by differing preferences of the aphids to the different plant genotypes and their resulting performance on these plants. Within the two host-plant diversity levels, aphid spatial distribution was influenced by an interaction among the aphid's own genotype, the genotype of a competing aphid, the origin of the parasitic plant population, and the host-plant genotype. Thus, the overall outcome involves both direct (i.e., host plant to aphid) and indirect (i.e., parasitic plant to aphid) interactions across all these species. These results show that a complex genetic environment influences the distribution of herbivores among host plants. Thus, in genetically diverse systems, interspecific genetic interactions between the host plant and herbivore can influence the population dynamics of the system and could also structure local communities. We suggest that direct and indirect genotypic interactions among species can influence community structure and processes. PMID:24558568

Zytynska, Sharon E; Frantz, Laurent; Hurst, Ben; Johnson, Andrew; Preziosi, Richard F; Rowntree, Jennifer K

2014-01-01

349

Bryophyte diaspore bank: a genetic memory? Genetic structure and genetic diversity of surface populations and diaspore bank in the liverwort Mannia fragrans (Aytoniaceae).  

PubMed

Propagule banks are assumed to be able to store considerable genetic variability. Bryophyte populations are expected to rely more heavily on stored propagules than those of seed plants due to the vulnerability of the haploid gametophyte. This reliance has important implications for the genetic structure and evolutionary potential of surface populations. A liverwort, Mannia fragrans, was used to test whether the bryophyte diaspore bank functions as a "genetic memory." If a diaspore bank is capable of conserving genetic variability over generations, the levels of genetic diversity in the soil are expected to be similar or higher than at the surface. Surface and diaspore bank constituents of two populations of M. fragrans were investigated. Genetic structure and diversity measured as unbiased heterozygosity were analyzed using three ISSR markers. Similar genetic diversities were found in the soil (H(s) = 0.067) and at the surface (H(s)= 0.082). However, more haplotypes and specific haplotype lineages were present in soil samples. The results suggest that the bryophyte diaspore bank has an important role in accumulating genetic variability over generations and seasons. It is postulated that the role of the diaspore bank as a "genetic memory" is especially important in species of temporarily available habitats that have long-lived spores and genetically variable populations. PMID:21632380

Hock, Zsófia; Szövényi, Péter; Schneller, Jakob J; Tóth, Zoltán; Urmi, Edwin

2008-05-01

350

Empirical Relationships between Species Richness, Evenness, and Proportional Diversity  

Microsoft Academic Search

Diversity (or biodiversity) is typically measured by a spe- cies count (richness) and sometimes with an evenness index; it may also be measured by a proportional statistic that combines both mea- sures (e.g., Shannon-Weiner index or ). These diversity measures ? H are hypothesized to be positively and strongly correlated, but this null hypothesis has not been tested empirically. We

Gray Stirling; Brian Wilsey

2001-01-01

351

Quantitative variation as a tool for detecting human-induced impacts on genetic diversity  

E-print Network

in biodiversity caused by different human-induced activities. We simulated a metapopulation setting under a number). The effects on diversity of these scenarios were assessed for neutral variation estimated from molecular; Genetic variance; Population genetic differentiation; Pollution; Bottlenecks; Mutation 1. Introduction

Rolán-Alvarez, Emilio

352

Amplified Fragment Length Polymorphism Marker-Based Genetic Diversity in Tamarind (Tamarindus indica)  

Microsoft Academic Search

Tamarindus indica, commonly called tamarind, is a medium-sized evergreen tree that gives a high yield. The fruit is commonly used as a spice. Despite its commercial importance in the international market, it has been little explored. The genetic diversity and genetic relatedness of 36 tamarind genotypes were studied using amplified fragment length polymorphism (AFLP) markers. Twelve primer pairs were used

Ali Qaid Ahmed Yahya Algabal; Narayanaswamy Papanna; Luke Simon

2011-01-01

353

The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos)  

E-print Network

that the Yellowstone grizzly bear has low levels of genetic variability compared with other Ursus arctos populationsThe history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation Craig R. Miller* and Lisette P. Waits Department of Fish

Kalinowski, Steven T

354

Examining the genetic diversity of Stipa grandis under various grazing pressures  

Microsoft Academic Search

The Stipa grandis steppe in the Inner Mongolia Autonomous Region occupies an area of 2798081 hm2. On the basis of the genetic variation, it was found that its adaptability to the environmental conditions under grazing pressure was significant. Using the Inter-Simple Sequence Repeat (ISSR) procedure, the changes to the genetic diversity of the Stipa grandis population under different grazing pressures

Dan Shan; Mengli Zhao; Bing Han; Guodong Han

2006-01-01

355

Genetic Diversity in Relation to Sexual and Asexual Reproduction in Populations of Melampsora larici-epitea  

Microsoft Academic Search

Genetic diversity of Melampsora larici-epitea leaf rust from three cultivated stands of the willow Salix viminalis was studied using AFLP polymorphisms at 60 loci. One population was located in Northern Ireland and two in Sweden. Analysis of molecular variance (AMOVA) showed that most of the genetic variation was distributed on a fine scale within the field in all populations. Both

Berit Samils; Valérie Stepien; Ulf Lagercrantz; Martin Lascoux; Urban Gullberg

2001-01-01

356

Genetics, Race, and Relatedness: Human Mobility and Human Diversity in the Genographic Project  

Microsoft Academic Search

The National Geographic Society's Genographic Project to reconstruct the geography of early human migration through analysis of the genetic material of indigenous people features a geographical imagination of human interconnection and diversity and differentiated human mobilities. It combines its central focus on human genetic difference with a simultaneous insistence on the progressive value of its explicitly antiracist message about shared

Catherine Nash

2011-01-01

357

Genetics, Race, and Relatedness: Human Mobility and Human Diversity in the Genographic Project  

Microsoft Academic Search

The National Geographic Society's Genographic Project to reconstruct the geography of early human migration through analysis of the genetic material of indigenous people features a geographical imagination of human interconnection and diversity and differentiated human mobilities. It combines its central focus on human genetic difference with a simultaneous insistence on the progressive value of its explicitly antiracist message about shared

Catherine Nash

2012-01-01

358

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and  

E-print Network

tuberculosis driven by genetic drift and human demography. PLoS Biol 6(12): e311. doi:10.1371/journalHigh Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography Ruth Hershberg1[ , Mikhail Lipatov1[ , Peter M. Small2,3 , Hadar Sheffer2 , Stefan Niemann4

Petrov, Dmitri

359

Compromising genetic diversity in the wild: unmonitored large-scale release  

E-print Network

is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated modified organisms; GMOs), (3) non-local populations of a species that occurs naturally at the release siteCompromising genetic diversity in the wild: unmonitored large-scale release of plants and animals

360

Genetic diversity in Hordeum chilense Roem. et Schult. germplasm collection as determined by endosperm storage proteins  

Microsoft Academic Search

Hordeum chilense Roem. et Schult. shows interesting characteristics for breeding, such as disease or pest resistance and has high variability for endosperm storage proteins, valuable for the improvement of the breadmaking quality of both tritordeum and wheat. Knowledge of the genetic structure and the level of H. chilense genetic diversity within its distribution zone may be important to decide on

S. G. Atienza; Z. Satovic; A. Martin; L. M. Martin

2005-01-01

361

High genetic diversity and population differentiation in Boechera fecunda , a rare relative of Arabidopsis  

Microsoft Academic Search

Conservation of endangered species becomes a critical issue with the increasing rates of extinction. In this study, we use 13 microsatellite loci and 27 single-copy nuclear loci to investigate the population genetics of Boechera fecunda, a rare relative of Arabidopsis thaliana, known from only 21 populations in Montana. We investigated levels of genetic diversity and population structure in comparison to

BAO-HUA SONG; THOMAS MITCHELL-OLDS

2007-01-01

362

A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases  

E-print Network

A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases Chao Templeton3 & Kevan M Shokat1 Chemical genetic analysis of protein kinases involves engineering kinases the necessary modification to the ATP binding pocket, as they lose catalytic activity or cellular function upon

Cai, Long

363

Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data  

PubMed Central

The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD), Landrace (CL) and Yorkshire (CY) swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity. PMID:25049847

Tang, G. Q.; Xue, J.; Lian, M. J.; Yang, R. F.; Liu, T. F.; Zeng, Z. Y.; Jiang, A. A.; Jiang, Y. Z.; Zhu, L.; Bai, L.; Wang, Z.; Li, X. W.

2013-01-01

364

Genetic diversity of wheat storage proteins and bread wheat quality  

Microsoft Academic Search

To understand the genetic and biochemical basis of the bread makingquality of wheat varieties, a large experiment was carried out with a set of162 hexaploid bread wheat varieties registered in the French or EuropeanWheat Catalogue. This material was used to analyse their allelic compositionat the twelve main storage protein loci. A large genetic and biochemicaldiversity of the gluten proteins was

G. Branlard; M. Dardevet; R. Saccomano; F. Lagoutte; J. Gourdon

2001-01-01

365

Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.  

PubMed

Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping. PMID:23291622

Pombert, Jean-François; Xu, Jinshan; Smith, David R; Heiman, David; Young, Sarah; Cuomo, Christina A; Weiss, Louis M; Keeling, Patrick J

2013-04-01

366

Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi  

PubMed Central

Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping. PMID:23291622

Pombert, Jean-Francois; Xu, Jinshan; Smith, David R.; Heiman, David; Young, Sarah; Cuomo, Christina A.; Weiss, Louis M.

2013-01-01

367

Genetic Diversity of Eukaryotic Microorganisms in Lake Taihu, a Large Shallow Subtropical Lake in China  

Microsoft Academic Search

We investigated the genetic diversity of eukaryotic microorganisms (0.8–20 ?m) by sequencing cloned 18S rRNA genes in six\\u000a genetic libraries constructed from six locations in Lake Taihu, a large shallow subtropical lake in China. Genetic libraries\\u000a of eukaryotic ribosomal RNA were screened by restriction fragment length polymorphism (RFLP) analysis, and one clone representative\\u000a of each RFLP pattern was partially sequenced. A

Meijun Chen; Feizhou Chen; Yang Yu; Jian Ji; Fanxiang Kong

2008-01-01

368

Analysis of genetic diversity in flowering dogwood natural stands using microsatellites: the effects of dogwood anthracnose  

Microsoft Academic Search

Flowering dogwood (Cornus florida L.) populations recently have experienced severe declines caused by dogwood anthracnose. Mortality has ranged from 48 to\\u000a 98%, raising the concern that genetic diversity has been reduced significantly. Microsatellite data were used to evaluate\\u000a the level and distribution of genetic variation throughout much of the native range of the tree. Genetic variation in areas\\u000a affected by

D. Hadziabdic; B. M. Fitzpatrick; X. Wang; P. A. Wadl; T. A. Rinehart; B. H. Ownley; M. T. Windham; R. N. Trigiano

2010-01-01

369

Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens  

PubMed Central

Background Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world. Results Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam. Conclusions Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted. PMID:24063717

2013-01-01

370

Genetic diversity and distribution of Peromyscus-borne hantaviruses in North America.  

PubMed Central

The 1993 outbreak of hantavirus pulmonary syndrome (HPS) in the southwestern United States was associated with Sin Nombre virus, a rodent-borne hantavirus; The virus' primary reservoir is the deer mouse (Peromyscus maniculatus). Hantavirus-infected rodents were identified in various regions of North America. An extensive nucleotide sequence database of an 139 bp fragment amplified from virus M genomic segments was generated. Phylogenetic analysis confirmed that SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America. Classic SNV is the major cause of HPS in North America, but other Peromyscine-borne hantaviruses, e.g., New York and Monongahela viruses, are also associated with HPS cases. Although genetically diverse, SNV-like viruses have slowly coevolved with their rodent hosts. We show that the genetic relationships of hantaviruses in the Americas are complex, most likely as a result of the rapid radiation and speciation of New World sigmodontine rodents and occasional virus-host switching events. PMID:10081674

Monroe, M. C.; Morzunov, S. P.; Johnson, A. M.; Bowen, M. D.; Artsob, H.; Yates, T.; Peters, C. J.; Rollin, P. E.; Ksiazek, T. G.; Nichol, S. T.

1999-01-01

371

RAPD analysis of the genetic diversity among accessions of Fabaceous forages (Poincianella spp) from the Caatinga.  

PubMed

Among members of the Fabaceae family, native to the Brazilian Caatinga, the species Poincianella pyramidalis and P. bracteosa exhibit particular potential as forage for cattle, sheep and goats. With the aim of establishing genetic relationships within Poincianella, random amplified polymorphic DNA analysis was performed on eight accessions of P. pyramidalis and two accessions of P. bracteosa, originating from the semiarid zone of the state of Piauí, northeastern Brazil, and present in the germplasm bank of Embrapa Meio Norte (Teresina, Piauí, Brazil). Amplification reactions using 11 selected arbitrary sequence primers generated 167 fragments with an overall polymorphism of 70.38%. Five monomorphic loci were generated exclusively in P. pyramidalis accessions, while three unique monomorphic loci were associated with P. bracteosa, and these represented potential species-specific markers. The similarity coefficients between Poincianella accessions were low (mean value 0.59) but with a wide variation (range 0.443 to 0.748). The similarity matrix and the dendrogram constructed using the unweighted pair group method allowed the separation of Poincianella accessions into two major clusters represented by the two distinct species, while the accessions of P. pyramidalis could be separated further into three subgroups. The high level of genetic diversity detected in the genus Poincianella could be used in future breeding programs to produce enhanced cultivars, although the variability could be better exploited if more specimens were collected from other locations within the semiarid region of northeastern Brazil. PMID:25117341

Mendes, R F M; Araujo Neto, R B; Nascimento, M P S B C; Lima, P S C

2014-01-01

372

Origin of Chinese Goldfish and Sequential Loss of Genetic Diversity Accompanies New Breeds  

PubMed Central

Background Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy–body shape, dorsal fin, eye shape, and tailfin–were selected for hypothesis-testing to identify those that better correspond to evolutionary history. Principal Finding Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of FST and Nm revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima’s D and Fu and Li’s D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher’s exact test identified matrilineal constraints on domestication. Conclusions Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy–Grass-goldfish, Egg-goldfish, and Wen-goldfish–better reflected the history of domestication. PMID:23527220

Wang, Shu-Yan; Luo, Jing; Murphy, Robert W.; Wu, Shi-Fang; Zhu, Chun-Ling; Gao, Yun; Zhang, Ya-Ping

2013-01-01

373

Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems.  

PubMed

Sorghum is a drought-tolerant crop with a vital role in the livelihoods of millions of people in marginal areas. We examined genetic structure in this diverse crop in Africa. On the continent-wide scale, we identified three major sorghum populations (Central, Southern, and Northern) that are associated with the distribution of ethnolinguistic groups on the continent. The codistribution of the Central sorghum population and the Nilo-Saharan language family supports a proposed hypothesis about a close and causal relationship between the distribution of sorghum and languages in the region between the Chari and the Nile rivers. The Southern sorghum population is associated with the Bantu languages of the Niger-Congo language family, in agreement with the farming-language codispersal hypothesis as it has been related to the Bantu expansion. The Northern sorghum population is distributed across early Niger-Congo and Afro-Asiatic language family areas with dry agroclimatic conditions. At a finer geographic scale, the genetic substructure within the Central sorghum population is associated with language-group expansions within the Nilo-Saharan language family. A case study of the seed system of the Pari people, a Western-Nilotic ethnolinguistic group, provides a window into the social and cultural factors involved in generating and maintaining the continent-wide diversity patterns. The age-grade system, a cultural institution important for the expansive success of this ethnolinguistic group in the past, plays a central role in the management of sorghum landraces and continues to underpin the resilience of their traditional seed system. PMID:25225391

Westengen, Ola T; Okongo, Mark Atam; Onek, Leo; Berg, Trygve; Upadhyaya, Hari; Birkeland, Siri; Kaur Khalsa, Siri Dharma; Ring, Kristoffer H; Stenseth, Nils C; Brysting, Anne K

2014-09-30

374

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

USGS Publications Warehouse

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

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

2008-01-01

375

Comparative population genomics in animals uncovers the determinants of genetic diversity.  

PubMed

Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies. PMID:25141177

Romiguier, J; Gayral, P; Ballenghien, M; Bernard, A; Cahais, V; Chenuil, A; Chiari, Y; Dernat, R; Duret, L; Faivre, N; Loire, E; Lourenco, J M; Nabholz, B; Roux, C; Tsagkogeorga, G; Weber, A A-T; Weinert, L A; Belkhir, K; Bierne, N; Glémin, S; Galtier, N

2014-11-13

376

Plasmodium falciparum populations from northeastern Myanmar display high levels of genetic diversity at multiple antigenic loci  

PubMed Central

Levels of genetic diversity of the malaria parasites and multiclonal infections are correlated with transmission intensity. In order to monitor the effect of strengthened malaria control efforts in recent years at the China-Myanmar border area, we followed the temporal dynamics of genetic diversity of three polymorphic antigenic markers msp1, msp2, and glurp in the Plasmodium falciparum populations. Despite reduced malaria prevalence in the region, parasite populations exhibited high levels of genetic diversity. Genotyping 258 clinical samples collected in four years detected a total of 22 PCR size alleles. Multiclonal infections were detected in 45.7% of the patient samples, giving a minimum multiplicity of infection of 1.41. The majority of alleles experienced significant temporal fluctuations through the years. Haplotype diversity based on the three-locus genotypes ranged from the lowest in 2009 at 0.33 to the highest in 2010 at 0.80. Sequencing of msp1 fragments from 36 random samples of five allele size groups detected 13 different sequences, revealing an additional layer of genetic complexity. This study suggests that despite reduced prevalence of malaria infections in this region, the parasite population size and transmission intensity remained high enough to allow effective genetic recombination of the parasites and continued maintenance of genetic diversity. PMID:23000544

Yuan, Lili; Zhao, Hui; Wu, Lanou; Li, Xiaomei; Parker, Daniel; Xu, Shuhui; Zhao, Yousheng; Feng, Guohua; Wang, Ying; Yan, Guiyun; Fan, Qi; Yang, Zhaoqing; Cui, Liwang

2012-01-01

377

Low genetic diversity in Melanaphis sacchari aphid populations at the worldwide scale.  

PubMed

Numerous studies have examined the genetic diversity and genetic structure of invading species, with contrasting results concerning the relative roles of genetic diversity and phenotypic plasticity in the success of introduced populations. Increasing evidence shows that asexual lineages of aphids are able to occupy a wide geographical and ecological range of habitats despite low genetic diversity. The anholocyclic aphid Melanaphis sacchari is a pest of sugarcane and sorghum which originated in the old world, was introduced into the Americas, and is now distributed worldwide. Our purpose was to assess the genetic diversity and structuring of populations of this species according to host and locality. We used 10 microsatellite markers to genotype 1333 individuals (57 samples, 42 localities, 15 countries) collected mainly on sugarcane or sorghum. Five multilocus lineages (MLL) were defined, grouping multilocus genotypes (MLG) differing by only a few mutations or scoring errors. Analysis of a 658 bp sequence of mitochondrial COI gene on 96 individuals revealed five haplotypes, with a mean divergence of only 0.19 %. The distribution of MLL appeared to be strongly influenced by geography but not by host plant. Each of the five MLL grouped individuals from (A) Africa, (B) Australia, (C) South America, the Caribbean and the Indian Ocean including East Africa, (D) USA, and (E) China. The MLL A and C, with a wide geographic distribution, matched the definition of superclone. Among aphids, M. sacchari has one of the lowest known rates of genetic diversity for such a wide geographical distribution. PMID:25148510

Nibouche, Samuel; Fartek, Benjamin; Mississipi, Stelly; Delatte, Hélène; Reynaud, Bernard; Costet, Laurent

2014-01-01

378

Genetic diversity and fitness in black-footed ferrets before and during a bottleneck.  

PubMed

The black-footed ferret (Mustela nigripes) is an endangered North American carnivore that underwent a well-documented population bottleneck in the mid-1980s. To better understand the effects of a bottleneck on a free-ranging carnivore population, we used 24 microsatellite loci to compare genetic diversity before versus during the bottleneck, and compare the last wild population to two historical populations. We also compared genetic diversity in black-footed ferrets to that of two sibling species, the steppe polecat (Mustela eversmanni) and the European polecat (Mustela putorius). Black-footed ferrets during the bottleneck had less genetic diversity than steppe polecats. The three black-footed ferret populations were well differentiated (F(ST) = 0.57 +/- 0.15; mean +/- SE). We attributed the decrease in genetic diversity in black-footed ferrets to localized extinction of these genetically distinct subpopulations and to the bottleneck in the surviving subpopulation. Although genetic diversity decreased, female fecundity and juvenile survival were not affected by the population bottleneck. PMID:12407208

Wisely, S M; Buskirk, S W; Fleming, M A; McDonald, D B; Ostrander, E A

2002-01-01

379

Low Genetic Diversity in Melanaphis sacchari Aphid Populations at the Worldwide Scale  

PubMed Central

Numerous studies have examined the genetic diversity and genetic structure of invading species, with contrasting results concerning the relative roles of genetic diversity and phenotypic plasticity in the success of introduced populations. Increasing evidence shows that asexual lineages of aphids are able to occupy a wide geographical and ecological range of habitats despite low genetic diversity. The anholocyclic aphid Melanaphis sacchari is a pest of sugarcane and sorghum which originated in the old world, was introduced into the Americas, and is now distributed worldwide. Our purpose was to assess the genetic diversity and structuring of populations of this species according to host and locality. We used 10 microsatellite markers to genotype 1333 individuals (57 samples, 42 localities, 15 countries) collected mainly on sugarcane or sorghum. Five multilocus lineages (MLL) were defined, grouping multilocus genotypes (MLG) differing by only a few mutations or scoring errors. Analysis of a 658 bp sequence of mitochondrial COI gene on 96 individuals revealed five haplotypes, with a mean divergence of only 0.19 %. The distribution of MLL appeared to be strongly influenced by geography but not by host plant. Each of the five MLL grouped individuals from (A) Africa, (B) Australia, (C) South America, the Caribbean and the Indian Ocean including East Africa, (D) USA, and (E) China. The MLL A and C, with a wide geographic distribution, matched the definition of superclone. Among aphids, M. sacchari has one of the lowest known rates of genetic diversity for such a wide geographical distribution. PMID:25148510

Nibouche, Samuel; Fartek, Benjamin; Mississipi, Stelly; Delatte, Helene; Reynaud, Bernard; Costet, Laurent

2014-01-01

380

The genetic diversity and spatial genetic structure of the Corso-Sardinian endemic Ferula arrigonii Bocchieri (Apiaceae).  

PubMed

Corsica and Sardinia represent major hotspots of plant diversity in the Mediterranean area and are priority regions for conservation due to their high number of endemic plant species. However, information supporting human decision-making on the conservation of these species is still scarce, especially at the genetic level. In this work, the first assessment is reported of the species-wide spatial genetic structure and diversity of Ferula arrigonii Bocchieri, a Corso-Sardinian endemic located in a few coastal sites and on small islands. Nine populations covering the entire natural range of the species were investigated by means of AFLP (amplified fragment length polymorphism) markers. Results indicate that this species is characterised by high levels of genetic polymorphism (92% polymorphic fragments) and of genetic diversity (H(w) = 0.317) and by relatively low differentiation among populations (F(st) = 0.057). PCoA, Bayesian analysis and neighbour-joining clustering were also employed to investigate the genetic structure of this species. Three genetically distinct groups were detected, although with considerable overlap between populations. PMID:24400949

Dettori, C A; Sergi, S; Tamburini, E; Bacchetta, G

2014-09-01

381

Genetic diversity within and among Lepidium draba populations from Eastern Anatolia based on RAPD analysis.  

PubMed

Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei's gene diversity value for all six populations was 0.1771. Shannon's information index varied with population (0.2278-0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G (ST)) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288. PMID:20496111

Aksakal, Ozkan; Sunar, Serap; Kaya, Yusuf; Agar, Guleray

2010-08-01

382

The stabilizing effects of genetic diversity on predator-prey dynamics  

PubMed Central

Heterogeneity among prey in their susceptibility to predation is a potentially important stabilizer of predator-prey interactions, reducing the magnitude of population oscillations and enhancing total prey population abundance. When microevolutionary responses of prey populations occur at time scales comparable to population dynamics, adaptive responses in prey defense can, in theory, stabilize predator-prey dynamics and reduce top-down effects on prey abundance. While experiments have tested these predictions, less explored are the consequences of the evolution of prey phenotypes that can persist in both vulnerable and invulnerable classes. We tested this experimentally using a laboratory aquatic system composed of the rotifer Brachionus calyciflorus as a predator and the prey Synura petersenii, a colony-forming alga that exhibits genetic variation in its propensity to form colonies and colony size (larger colonies are a defense against predators). Prey populations of either low initial genetic diversity and low adaptive capacity or high initial genetic diversity and high adaptive capacity were crossed with predator presence and absence. Dynamics measured over the last 127 days of the 167-day experiment revealed no effects of initial prey genetic diversity on the average abundance or temporal variability of predator populations. However, genetic diversity and predator presence/absence interactively affected prey population abundance and stability; diversity of prey had no effects in the absence of predators but stabilized dynamics and increased total prey abundance in the presence of predators. The size structure of the genetically diverse prey populations diverged from single strain populations in the presence of predators, showing increases in colony size and in the relative abundance of cells found in colonies. Our work sheds light on the adaptive value of colony formation and supports the general view that genetic diversity and intraspecific trait variation of prey can play a vital role in the short-term dynamics and stability of planktonic predator-prey systems. PMID:25339982

Steiner, Christopher F; Masse, Jordan

2013-01-01

383

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers.  

PubMed

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity. PMID:16734682

SanCristobal, M; Chevalet, C; Peleman, J; Heuven, H; Brugmans, B; van Schriek, M; Joosten, R; Rattink, A P; Harlizius, B; Groenen, M A M; Amigues, Y; Boscher, M-Y; Russell, G; Law, A; Davoli, R; Russo, V; Dèsautés, C; Alderson, L; Fimland, E; Bagga, M; Delgado, J V; Vega-Pla, J L; Martinez, A M; Ramos, M; Glodek, P; Meyer, J N; Gandini, G; Matassino, D; Siggens, K; Laval, G; Archibald, A; Milan, D; Hammond, K; Cardellino, R; Haley, C; Plastow, G

2006-06-01

384

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

USGS Publications Warehouse

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

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

2012-01-01

385

Extensive Genetic Diversity, Unique Population Structure and Evidence of Genetic Exchange in the Sexually Transmitted Parasite Trichomonas vaginalis  

PubMed Central

Background Trichomonas vaginalis is the causative agent of human trichomoniasis, the most common non-viral sexually transmitted infection world-wide. Despite its prevalence, little is known about the genetic diversity and population structure of this haploid parasite due to the lack of appropriate tools. The development of a panel of microsatellite makers and SNPs from mining the parasite's genome sequence has paved the way to a global analysis of the genetic structure of the pathogen and association with clinical phenotypes. Methodology/Principal Findings Here we utilize a panel of T. vaginalis-specific genetic markers to genotype 235 isolates from Mexico, Chile, India, Australia, Papua New Guinea, Italy, Africa and the United States, including 19 clinical isolates recently collected from 270 women attending New York City sexually transmitted disease clinics. Using population genetic analysis, we show that T. vaginalis is a genetically diverse parasite with a unique population structure consisting of two types present in equal proportions world-wide. Parasites belonging to the two types (type 1 and type 2) differ significantly in the rate at which they harbor the T. vaginalis virus, a dsRNA virus implicated in parasite pathogenesis, and in their sensitivity to the widely-used drug, metronidazole. We also uncover evidence of genetic exchange, indicating a sexual life-cycle of the parasite despite an absence of morphologically-distinct sexual stages. Conclusions/Significance Our study represents the first robust and comprehensive evaluation of global T. vaginalis genetic diversity and population structure. Our identification of a unique two-type structure, and the clinically relevant phenotypes associated with them, provides a new dimension for understanding T. vaginalis pathogenesis. In addition, our demonstration of the possibility of genetic exchange in the parasite has important implications for genetic research and control of the disease. PMID:22479659

Conrad, Melissa D.; Gorman, Andrew W.; Schillinger, Julia A.; Fiori, Pier Luigi; Arroyo, Rossana; Malla, Nancy; Dubey, Mohan Lal; Gonzalez, Jorge; Blank, Susan; Secor, William E.; Carlton, Jane M.

2012-01-01

386

Genetic Diversity and Population Structure of Sitodiplosis mosellana in Northern China  

PubMed Central

The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (FST?=?0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (FST?=?0.116, Nm?=?1.89) than those in the eastern group (FST?=?0.049, Nm?=?4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r?=?0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs. PMID:24265688

Duan, Yun; Wu, Yu-qing; Luo, Li-zhi; Miao, Jin; Gong, Zhong-jun; Jiang, Yue-li; Li, Tong

2013-01-01

387

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus  

PubMed Central

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

Furlan, Elise; Stoklosa, J; Griffiths, J; Gust, N; Ellis, R; Huggins, R M; Weeks, A R

2012-01-01

388

Genetic Diversity in Hypericum and AFLP Markers for Species-Specific Identification of H. perforatum L.  

PubMed Central

One of the top-selling medicinal products worldwide is Hypericum perforatum (St. John's Wort). Despite its cosmopolitan distribution and utilization, little is known regarding the relationship of the bioactive compounds in H. perforatum to the plants from which they are purportedly derived. In this study, amplified fragment length polymorphism (AFLP) analysis of 56 Hypericum accessions, representing 11 species, was conducted to gain a better understanding of diversity within Hypericum species, especially within cultivated accessions of H. perforatum, and to establish a molecular methodology that will provide breeders and regulators with a simple, affordable, and accurate tool with which to identify purported H. perforatum material. Utilizing four primer combinations, a total of 298 polymorphic markers were generated, of which 17 were present in all H. perforatum accessions and 2 were specific to only H. perforatum. This study demonstrates that AFLP can be utilized not only to determine the relationships of closely related Hypericum accessions, but as a tool to authenticate material in herbal remedies through the use of genetic fingerprinting. PMID:18072074

Percifield, Ryan J.; Hawkins, Jennifer S.; McCoy, Joe-Ann; Widrlechner, Mark P.; Wendel, Jonathan F.

2008-01-01

389

Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin  

PubMed Central

Background Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secon