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1

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

PubMed

The spectacular diversity in size, conformation, and pelage that characterizes the domestic dog reflects not only the intensity of artificial selection but ultimately the genetic variability of founding populations. Here we review past molecular genetic data that are relevant to understanding the origin and phylogenetic relationships of the dog. DNA-DNA hybridization data show that the dog family Canidae diverged about 50 million years ago from other carnivore families. In contrast, the extant canids are very closely related and diverged from a common ancestor about 10 million years ago. The evidence supporting a close relationship of dogs with gray wolves is overwhelming. However, dogs are remarkably diverse in mitochondrial and nuclear genes. Mitochondrial DNA analysis suggests a more ancient origin of dogs than has been indicated by the fossil record. In addition, dogs have originated from or interbred with wolves throughout their history at different times and different places. We test the possibility of an independent domestication event in North America by analysis of mtDNA variation in the Xoloitzcuintli. This unusual breed is believed to have been kept isolated for thousands of years and may be one of the most ancient breeds in North America. Our results do not support a New World domestication of dogs nor a close association of the Xoloitzcuintli with other hair-less breeds of dogs. Despite their phenotypic uniformity, the Xoloitzcuintli has a surprisingly high level of mtDNA sequence variation. Other breeds are also genetically diverse, suggesting that dog breeds were often founded with a large number of dogs from outbred populations. PMID:9987908

Vilà, C; Maldonado, J E; Wayne, R K

2

Genetic diversity, structure, and breed relationships in Iberian cattle.  

PubMed

In Iberia there are 51 officially recognized cattle breeds of which 15 are found in Portugal and 38 in Spain. We present here a comprehensive analysis of the genetic diversity and structure of Iberian cattle. Forty of these breeds were genotyped with 19 highly polymorphic microsatellite markers. Asturiana de los Valles displayed the greatest allelic diversity and Mallorquina the least. Unbiased heterozygosity values ranged from 0.596 to 0.787. The network based on Reynolds distances was star-shaped with few pairs of interrelated breeds and a clear cluster of 4 breeds (Alistana/Arouquesa/Marinhoa/Mirandesa). The analysis of the genetic structure of Iberian cattle indicated that the most probable number of population clusters included in the study would be 36. Distance results were supported by the STRUCTURE software indicating a relatively recent origin or possible crossbreeding or both between pairs or small groups of breeds. Five clusters included 2 different breeds (Betizu/Pirenaica, Morucha/Avileña, Parda de Montaña/Bruna de los Pirineos, Barrosã/Cachena, and Toro de Lidia/Brava de Lide), 3 breeds (Berrenda en Negro, Negra Andaluza, and Mertolenga) were divided in 2 independent clusters each, and 2 breeds were considered admixed (Asturiana de los Valles and Berrenda en Colorado). Individual assignation to breeds was not possible in the 2 admixed breeds and the pair Parda de Montaña/Bruna de los Pirineos. The relationship between Iberian cattle reflects their geographical origin rather than their morphotypes. Exceptions to this geographic clustering are most probably a consequence of crossbreeding with foreign breeds. The relative genetic isolation within their geographical origin, the consequent genetic drift, the adaptation to specific environment and production systems, and the influence of African and European cattle have contributed to the current genetic status of Iberian cattle, which are grouped according to their geographical origin. The greater degree of admixture observed in some breeds should be taken into account before using molecular markers for genetic assignment of individuals to breeds. PMID:21415418

Martín-Burriel, I; Rodellar, C; Cañón, J; Cortés, O; Dunner, S; Landi, V; Martínez-Martínez, A; Gama, L T; Ginja, C; Penedo, M C T; Sanz, A; Zaragoza, P; Delgado, J V

2011-04-01

3

Genetic diversity and genetic relationship of Caragana microphylla, Caragana davazamcii and Caragana korshinskii on the Inner Mongolia Plateau, China  

Microsoft Academic Search

C. microphylla, C. davazamcii and C. korshinskii exhibit a geographical replacement series from east to west on the Inner Mongolia Plateau. Currently, there is still a debate about the taxonomic and genetic relationship among these 3 species. We studied the genetic diversity and genetic relationship among these 3 species by analyzing DNA samples of individual plants from within 10 populations

Guo Hongyu; Gao Yubao; Ma Chengcang; Ren Anzhi; Wu Jianbo; Wang Yinhua

2008-01-01

4

DEVELOPMENT OF AQUATIC MODELS FOR TESTING THE RELATIONSHIP BETWEEN GENETIC DIVERSITY AND POPULATION EXTINCTION RISK  

EPA Science Inventory

The relationship between population adaptive potential and extinction risk in a changing environment is not well understood. Although the expectation is that genetic diversity is directly related to the capacity of populations to adapt, the statistical and predictive aspects of ...

5

Evaluation of Lespedeza germplasm genetic diversity and its phylogenetic relationship with the genus Kummerowia  

Microsoft Academic Search

The genetic diversity of the genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers\\u000a derived from Medicago, cowpea and soybean were used to assess the genetic diversity of the USDA Lespedeza germplasm collection and clarify its

M. L. Wang; J. A. Mosjidis; J. B. Morris; Z. B. Chen; N. A. Barkley; G. A. Pederson

2009-01-01

6

Contrasting relationships between species diversity and genetic diversity in natural and disturbed forest tree communities.  

PubMed

• This study aimed to reveal species-genetic diversity correlations (SGDCs) and their underlying mechanisms in natural and disturbed forests. • A community survey and molecular analyses were carried out to compare species diversity (SD), the genetic diversity of the dominant tree species Euptelea pleiospermum (GD), the altitudinal patterns of SD and GD, SGDC, genetic differentiation (F(ST) ), community divergence (F(ST) -C), effective population size (N(e) ), and recent migration rate between mountain riparian forests along the Yandu (natural) and Nan (disturbed) rivers. • In natural forests, both SD and GD showed a unimodal altitudinal pattern and GD was positively correlated with SD, whereas a unimodal pattern and positive SGDC were not found in the disturbed forests. SD and F(ST) at the natural sites were higher than those at the disturbed sites. However, there were no significant differences in GD, F(ST) -C, N(e) or recent migration rate between the natural and disturbed sites. • A correlation between the patterns of SD and GD along a geographical gradient (e.g. altitude) is an important driver of positive SGDC. The absence of positive SGDC in the disturbed forests may result from reduced SD but unaffected GD, indicating nonparallel changes in SD and GD. This study furthermore cautions against generalizations about changes in SD and GD following disturbance. PMID:22106986

Wei, Xinzeng; Jiang, Mingxi

2011-11-22

7

Assessment of genetic diversity and relationships among Coix lacryma-jobi accessions using microsatellite markers  

Microsoft Academic Search

The present study describes the assessment of genetic diversity and relationships among 79 Job’s tears (Coix lacrymajobi L.) accessions collected from China and Korea using 17 microsatellite markers. A total of 57 alleles were detected with an\\u000a average of 3.4 alleles per locus. A high frequency of rare alleles (36.3 %) was observed within the collection. Values for\\u000a observed (HO),

K.-H. Ma; K.-H. Kim; A. Dixit; I.-M. Chung; J.-G. Gwag; T.-S. Kim; Y.-J. Park

2010-01-01

8

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

9

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

10

Phylogenetic relationship among related genera of Plumbaginaceae and preliminary genetic diversity of Limonium sinense in China.  

PubMed

Phylogenetic relationship of Limonium and other genera of Plumbaginaceae in China were studied using the cp rbcL, matK and the intergene spacer of trnL-trnF. The analysis showed that Plumbaginaceae was strongly supported monophyletic group sister to Polygonacea, and two tribes were comfirmed by phylogenetic analysis in Plumbaginaceae. Preliminary genetic diversity of Limonium sinense in China was also analyzed in this study by nrDNA (ITS) and cp DNA (two regions of intergenic spacers, trnL-trnF and psbA-trnH). The results showed that the population genetic diversity was low perhaps for human activities and breeding system of this species. These results have been used to understand the evolutionary and demographic history of L. sinense, which is a requisite to establish efficient conservation measures for this species. PMID:22759517

Ding, Ge; Zhang, Daizhen; Yu, Yanqiu; Zhao, Lingling; Zhang, Beibei

2012-06-30

11

[Microsatellite analysis of genetic diversity and phylogenetic relationship of nine species of grouper in genus Epinephelus].  

PubMed

Thirteen microsatellite markers of Epinephelus awoara previously discovered by our lab were selected to analyze the genetic diversity and phylogenetic relationship of nine species of grouper (E. awoara, E. merra, E. fario, E. fasciatus, E. lanceolatus, E. akaara, E. septemfasciatus, E. coioides and E. fuscoguttatus) from South China Sea. The results showed that the number of total alleles of these 13 microsatellite loci was 84 in these fishes, the mean number of alleles ranged from 2.69 to 5.38, mean polymorphism information content (PIC) ranged from 0.1976 to 0.4267, mean observed heterozygosity (Ho) from 0.4615 to 0.6239, mean expected heterozygosity (He) from 0.3510 to 0.4754 and mean Hardy-Weinberg departure value (D) from 0.1097 to 0.2836, respectively. All of these indicated that genetic diversity of the nine species of grouper was at a medium level. Two NJ dendrograms showed that E. coioides, E. fuscoguttatus and E. lanceolatus were grouped together, while E. awoara, E. akaara and E. septemfasciatus were in a second group, and E. merra, E. fasciatus and E. fario were in a third group which had a relatively closed relationship with the second group. The dendrograms could also support a conclusion that Promicrops lanceolatus (E. lanceolatus) should be included in genus Epinephelus. PMID:17646150

Dong, Qiu-Fen; Liu, Chu-Wu; Guo, Yu-Song; Liu, Li; Wu, Yong

2007-07-01

12

Allozyme analysis of genetic diversity, genetic structure and interspecific relationship in genus Eriobotrya  

Microsoft Academic Search

SUMMARY - Levels of allozyme diversity were determined in Eriobotrya populations. 24 loci for 12 enzyme systems of 120 materials from 4 species and 1 variant species: E. japonica Lindl., E. prinoides Rehd. et Wils., E. serrata Vidal., E. dayaoshanensis Chen and E. prinoides var. daduheensis H.Z. Zhang, were investigated using isoelectric focus in thin-layer polyacrylamide slab gel. Fifty nine

L. H. Cai; H. W. Huang; X. X. Deng; W. C. Zhang

13

Phylogenetic relationships and genetic diversity of the USDA Vigna germplasm collection revealed by gene-derived markers and sequencing.  

PubMed

Phylogenetic relationships in the USDA Vigna germplasm collection are somewhat unclear and their genetic diversity has not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 gene-derived markers from legumes were employed. Some high-quality amplicons were sequenced. Indels (insertion/deletions) were discovered from the sequence alignments that were specific identifiers for some Vigna species. With regard to revealing polymorphisms, intron-spanning markers were more effective than exon-derived markers. These gene-derived markers were more successful in revealing interspecific polymorphisms than intraspecific polymorphisms at both the DNA fragment and sequence levels. Two different dendrograms were generated from DNA fragment data and sequence data, respectively. The results from these two dendrograms supported each other and showed similar phylogenetic relationships among the Vigna species investigated. The accessions clustered into four main groups and 13 subgroups. Each subgroup represents a subgenus or a species. Phylogenetic analysis revealed that an accession might be misclassified in our collection. The putative misclassified accession was further supported by seed morphology. Limited intraspecific genetic diversity was revealed by these gene-derived markers and/or sequences. The USDA Vigna germplasm collection currently consists of multiple species with many accessions further classified into specific subspecies, but very few subspecies of the total subspecies available exist within the collection. Based on our results, more attention should be paid to the subspecies, wild forms and/or botanical varieties for future curation in order to expand the genetic diversity of Vigna germplasm in the USDA collection. PMID:19123965

Wang, Ming Li; Barkley, Noelle A; Gillaspie, Graves A; Pederson, Gary A

2008-12-01

14

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

PubMed

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 the female figs present in Turkish genetic resources, using 157 molecular genome markers including 129 sequence-related amplified polymorphisms, 21 random amplified polymorphic DNAs, and 7 simple-sequence repeats. The plant samples mainly included Turkish fig collections selected throughout the country over the course of a half-century. Neighbor-joining analysis revealed continuous dissimilarity range, and it was difficult to classify figs into distinct groups. The principle component analysis produced similar results. The analysis of molecular variance indicated that 95 and 93% of genetic variation were explained by within geographic origins and similar fruit rind color, respectively. Sub-structuring Bayesian analysis assigned the 96 female figs into four sub-populations, and indicated that they were highly related. The corrected allelic pairwise distances among the six geographic origins were less than 5%. This study suggests that geography- and color-based groups were not genetically distinct among the Turkish figs. PMID:19711187

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

2009-08-27

15

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers.  

PubMed

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera. PMID:16094440

Barkley, N A; Newman, M L; Wang, M L; Hotchkiss, M W; Pederson, G A

2005-08-01

16

GENETIC DIVERSITY IN AVOCADO  

Microsoft Academic Search

People working on avocado germplasm improvement are more fortunate than those work- ing with some other crops (mango for one important example) in that Persea americana in its many genotypes presents a wide variety of genetic diversity. This is probably because avocados evolved in a part of North and Central America characterized itself by consider- able diversity in climates, related

Robert J. Knight

1999-01-01

17

Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types.  

PubMed

More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses. PMID:23997181

Chouhy, Diego; Bolatti, Elisa M; Pérez, Germán R; Giri, Adriana A

2013-08-30

18

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

PubMed

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 (F ST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, F ST 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 (F ST) 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

2013-03-21

19

[Genetic diversity and phylogenetic relationships in the zokor subfamily Myospalacinae (Rodentia, Muridae) inferred from RAPD-PCR].  

PubMed

Zokors (Myospalacinae) is a group of rodents specialized for underground life, endemics of eastern Asia, which is taxonomically and evolutionarily poorly studied. We examined genetic diversity and phylogenetic relationships among zokors (Myospalax myospalax, Myospalax aspalax, Myospalax armandii, Myospalax psilurus, Myospalax smithii) using RAPD-PCR. The subfamily Myospalacinae was shown to be monophyletic and contain four evolutionary branches: M. myospalax, M. aspalax-M. armandii, M. smithii and M. psilurus. Genetic differences and high differentiation were found among the species and between two geographic forms of Manjurian zokor M. psilurus from the marginal parts of the range, Transbaikalia and Primorye. The psiluris phylogroup was shown to be dichotomically divided into two clades according to the geographical distribution of animals from Transbaikalia and Primorye. The genetic differentiation between the geographic forms of M. psilurus corresponded to the differentiation between morphologically similar species M. aspalax and M. armandii. M. armandii is a sister taxon with regard to M. aspalax. This new evidence on the evolutionary relationships among zokors does not contradict the traditional views inferred from morphological, karyological, and allozyme data, on isolation of M. myospalax and the character of form development in this group. The species status of Myospalax psilurus Milne-Edwards, 1874, M. epsilanus Thomas, 1912, M. armandii Milne-Edwards, 1867, which had been suggested earlier on the basis of biochemical and karyological data, was confirmed. PMID:21516793

Tsvirka, M V; Pavlenko, M V; Korablev, V P

2011-02-01

20

Analysis of the genetic diversity of the lymphocystis virus and its evolutionary relationship with its hosts.  

PubMed

Lymphocystis disease virus (LCDV) is the causative agent of lymphocystis disease. In this study, the mcp gene of LCDV and the cyt b gene of the host fish were selected as molecular markers, and the phylogenetic relationships between LCDV and its host were analyzed. The 25 LCDV isolates examined in this study were attributed to seven LCDV genotypes: genotype I (LCDV-1), genotype II (LCDV-cn, etc.), genotype III (LCDV-rf), genotype IV (LCDV-rc and LCDV-sb), genotype V (LCDV-cb), genotype VI (LCDV-tl), and genotype VII (LCDV-sa). Genotype VII is a new genotype. LCDV1 was found to have differentiated first, followed by LCDV-rf; then LCDV-tl; LCDV-cb; and then LCDV-sa; and by LCDV-rc and LCDV-sb; and finally by LCDV-cn, LCDV-C, and LCDV-jf. From the host evolutionary perspective, Rachycentron canadum was found to have differentiated first, followed by Trichogaster leeri, Chanda baculis, and Sebastes schlegeli, Lateolabrax sp., Sparus aurata, Platichthys flesus, and Paralichthys olivaceus. Comparison of the phylogenies of the host fish species and LCDVs revealed no significant evidence of cospeciation between LCDVs and their host fish. In-depth studies of the genetic variation in LCDVs can enhance our understanding of the mechanism of LCDV infection, which may provide important insights into the prevention and treatment of lymphocystis disease. PMID:21805162

Yan, Xiu-Ying; Wu, Zao-He; Jian, Ji-Chang; Lu, Yi-Shan; Sun, Xiu-Qin

2011-07-30

21

GENETIC DIVERSITY OF GARLIC  

Technology Transfer Automated Retrieval System (TEKTRAN)

Garlic (Allium sativum L.) is valued for its culinary and neutraceutical qualities. Farmers grow hundreds of differently named garlic accessions in the United States. A genetic analysis was performed to determine the extent of duplication and diversity across these garlic accessions. Phenotypically ...

22

Genetic diversity and relationships among Lablab purpureus genotypes evaluated using RAPD as markers  

Microsoft Academic Search

Genetic variation in 40 accessions of Lablab purpureus was evaluated using random amplified polymorphic DNA as markers. A high level of genetic variation in this species was detected but this was mainly restricted to the difference between cultivated and wild forms. Of the cultivated genotypes, genetic variation among Asian collections was significantly higher than that among African collections. The three

C. J. Liu

1996-01-01

23

Is there a trade-off between species diversity and genetic diversity in forest tree communities?  

Microsoft Academic Search

The two most important components of biodiversity, species diversity and genetic diversity, have generally been treated as separate topics, although a coordination between both components is believed to be critical for ecosystem stability and resilience. Based on a new trait concept that allows for the assessment of genetic diversity across species, the relationship between species diversity and genetic diversity was

Christian Wehenkel; Fritz Bergmann; Hans-Rolf Gregorius

2006-01-01

24

Genetic diversity within the morphological species Giardia intestinalis and its relationship to host origin  

Microsoft Academic Search

A genetic analysis of Giardia intestinalis, a parasitic protozoan species that is ubiquitous in mammals worldwide, was undertaken using organisms derived from a variety of mammalian hosts in different geographical locations. The test panel of 53 Giardia isolates comprised 48 samples of G. intestinalis, including representatives of all known genetic subgroups, plus an isolate of G. ardeae and four isolates

Paul T. Monis; Ross H. Andrews; Graham Mayrhofer; Peter L. Ey

2003-01-01

25

The relationship between genetic and chemotypic diversity in American ginseng (Panax quinquefolius L.).  

PubMed

Ginseng is one of the world's most important herbals used as an adaptogen and a cure for an impressively large range of ailments. Differences in the medicinal properties of ginseng roots have been attributed to variation in ginsenoside composition. In this study, the association between genetic and chemotypic profiles of wild and cultivated American ginseng (Panax quinquefolius L.) roots grown in Maryland was investigated. Ginseng roots were classified into chemotypes based on their relative composition of Re and Rg1. Genetic profiles of these roots were determined from the analysis of 38 polymorphic RAPD markers and used for a cluster analysis of genetic similarities. The close correspondence between chemotype and genetic cluster provides the first DNA-based evidence for the genetic basis of ginsenoside composition. Results of this research are significant for plant breeding and conservation, phytochemical research, and clinical and pharmacological studies. Also, the correlation between RAPD markers and chemotype indicates the potential to use RAPD markers as a reliable and practical method for identification and certification of ginseng roots. PMID:23591019

Schlag, Erin M; McIntosh, Marla S

2013-04-13

26

Genetic diversity of \\  

Microsoft Academic Search

The commonly known Pimenta longa is a commercially valuable natural resource found wild in Acre, Brazil. Specifically, three Piperaceae species with contested taxonomic status were studied, Piper hispidinervum, Piper aduncum, and Piper hispidum, to assesses the inter- and intra-specific genetic relationship of 49 Piper genotypes kept in the Pimenta longa germplasm collection at Embrapa Acre, using sixty six Random Amplified

Lúcia Helena de Oliveira Wadt; Christiane Ehringhaus; Paulo Yoshio Kageyama

2004-01-01

27

Metabolomic diversity in the species Escherichia coli and its relationship to genetic population structure  

Microsoft Academic Search

The genomic richness and intra-species heterogeneity of the prokaryotic world is suggestive of extensive biochemical diversity.\\u000a In this study, metabolomic profiling permitted a phylogenetic assessment of metabolic diversification amongst environmental,\\u000a medical and laboratory strains of Escherichia coli. Strikingly, no two E. coli isolates exhibited the same metabolite pool profile. Only 27% of detected metabolite spots in 2-dimensional high-performance\\u000a thin layer

Ram Prasad Maharjan; Thomas Ferenci

2005-01-01

28

A perspective on positive relationships between genetic diversity and abundance in fishes.  

PubMed

Given over 90 combined years in academic and professional activities related to genetics and fishery management (FU 57, JS 36-see Waples et al. 2008), we are pleased to provide an invited perspective generated by the interesting and useful article of McCusker & Bentzen (2010). These authors reaffirm the apparent signature of neutrality of mitochondrial and microsatellite markers through an exhaustive analysis of archived genotypic data for 105 marine and freshwater fishes. They note that their conclusions are consistent with earlier and less comprehensive analyses and that they do not exclude the operation of some selective activity (e.g. genetic 'draft'), which may be overwhelmed by N(e) -related stochastic processes. Here, we provide a complementary focus, recalling relevant issues related to neutrality and selection in applications of molecular variations in fishery management. PMID:21050291

Utter, Fred; Seeb, James

2010-11-01

29

Assessment of genetic diversity and genetic relationships among 29 populations of Azadirachta indica A. Juss. using RAPD markers  

Microsoft Academic Search

Randomly amplified polymorphic DNA (RAPD) analysis was employed to assess genetic divergence among 29 neem accessions collected from two agro-ecological regions of India (11 agro-climatic sub-zones), which cover three states, Punjab, Haryana and Rajasthan. Out of 24, 10-mer random primers used for studying genetic divergence, 14 were polymorphic, generating a total of 73 amplification products with an average of 5.21

R. P. Singh Deshwal; Rakesh Singh; Kanika Malik; G. J. Randhawa

2005-01-01

30

The use of RAPD markers for detecting genetic diversity, relationship and molecular identification of Chinese elite tea genetic resources [ Camellia sinensis (L.) O. Kuntze] preserved in a tea germplasm repository  

Microsoft Academic Search

The genetic diversity, relationship and molecular identification of 15 well known, widely planted traditional Chinese elite tea genetic resources [Camellia sinensis (L.) O. Kuntze] preserved in the China National Germplasm Hangzhou Tea Repository in the Tea Research Institute of the Chinese Academy of Agricultural Sciences located in Zhejiang province, China, were investigated using RAPD markers. A total of 1050 bands

Liang Chen; Qi-kang Gao; Da-ming Chen; Chang-jie Xu

2005-01-01

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.

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

2007-01-01

32

Genetic diversity and disease susceptibility.  

PubMed Central

The range of genetic diversity within human populations is enormous. Genetic susceptibility to common chronic disease is a significant part of this genetic diversity, which also includes a variety of rare clear-cut inherited diseases. Modern DNA-based genomic analysis can now routinely lead to the identification of genes involved in disease susceptibility, provides the basis for genetic counselling in affected families, and more widely for a genetically targeted approach to disease prevention. This naturally raises problems concerning the use of information on an individual's decisions, but for employment, and health and life insurance.

Bodmer, W F

1997-01-01

33

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

PubMed

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

Sagnard, Fabrice; Deu, Monique; Dembélé, Dékoro; Leblois, Raphaël; Touré, Lassana; Diakité, Mohamed; Calatayud, Caroline; Vaksmann, Michel; Bouchet, Sophie; Mallé, Yaya; Togola, Sabine; Traoré, Pierre C Sibiry

2011-08-03

34

Genetic Diversity among the Arabs  

Microsoft Academic Search

The Arabs in general are genetically diverse. Major factors that contributed to their diversity include the migrations of Semitic tribes from the Arabian Peninsula, the Islamic expansion in the 7th century AD, the Crusade wars and the recent migration dynamics. These events have resulted in the admixture of the original Arabs with other populations extending from east and south Asia

Ahmad S. Teebi; Saeed A. Teebi

2005-01-01

35

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

36

Genetic Diversity of Toscana Virus  

PubMed Central

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

Collao, Ximena; Palacios, Gustavo; Sanbonmatsu-Gamez, Sara; Perez-Ruiz, Mercedes; Negredo, Ana I.; Navarro-Mari, Jose-Maria; Grandadam, Marc; Aransay, Ana Maria; Lipkin, W. Ian; Tenorio, Antonio

2009-01-01

37

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

38

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

39

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.

Richards, Zoe T; Oppen, Madeleine J H

2012-01-01

40

Rarity and genetic diversity in Indo-Pacific Acropora corals.  

PubMed

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

2012-07-06

41

Genetic Diversity among Enterococcus faecalis  

Microsoft Academic Search

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.

Shonna M. McBride; Vincent A. Fischetti; Donald J. Leblanc; Robert C. Moellering; Michael S. Gilmore; Leah Cowen

2007-01-01

42

Genetic Diversity Increases Insect Herbivory on Oak Saplings  

PubMed Central

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

Castagneyrol, Bastien; Lagache, Lelia; Giffard, Brice; Kremer, Antoine; Jactel, Herve

2012-01-01

43

An AFLP-based survey of genetic diversity and relationships of major farmed cultivars and geographically isolated wild populations of Saccharina japonica (Phaeophyta) along the northwest coasts of the Pacific  

Microsoft Academic Search

The genetic diversity and relationships of six representative cultivars and six geographically isolated wild populations\\u000a of Saccharina japonica along the northwest coasts of the Pacific Ocean were investigated using AFLP markers. A total of 547 bands were generated\\u000a across all samples by ten primer combinations. At the cultivar or population level, the percentage of polymorphic loci (P), gene diversity (H),

Ti Feng Shan; Shao Jun Pang; Yu Rong Zhang; Irina M. Yakovleva; Anna V. Skriptsova

2011-01-01

44

Genetic diversity among the Arabs.  

PubMed

The Arabs in general are genetically diverse. Major factors that contributed to their diversity include the migrations of Semitic tribes from the Arabian Peninsula, the Islamic expansion in the 7th century AD, the Crusade wars and the recent migration dynamics. These events have resulted in the admixture of the original Arabs with other populations extending from east and south Asia to Europe and Africa. Their demographic features include high rates of consanguinity, a large family size and a rapid population growth. There is a high frequency of autosomal recessive disorders and increased frequencies of homozygosity for autosomal dominant traits, such as familial hypercholesterolemia and X-linked traits, such as glucose-6-phosphate dehydrogenase deficiency. The patterns of autosomal recessive disorders, including their mutations, may be different in various geographic locations within the Arab world. However, there are disorders that are specifically prevalent among the Arabs either uniformly or in certain locations. The Arab Genetic diseases include Bardet-Biedl syndrome, Meckel syndrome, autosomal recessive severe childhood muscular dystrophy, osteopetrosis and renal tubular acidosis, Sanjad-Sakati syndrome and others. PMID:15767750

Teebi, Ahmad S; Teebi, Saeed A

2005-01-01

45

Genetic Diversity in Chinese melon (Cucumis melo L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

46

Genetic diversity of NS5A protein from hepatitis C virus genotype 3a and its relationship to therapy response  

PubMed Central

Background The quasispecies nature of HCV may have important implications for viral persistence, pathogenicity and resistance to antiviral agents. The variability of one of the viral proteins, NS5A, is believed to be related to the response to IFN therapy, the standard treatment for infection. In this study we analyzed the quasispecies composition of NS5A protein in patients infected with HCV genotype 3a, before IFN therapy. Methods Viral RNA was isolated from samples of 12 patients: four sustained virological responders (SVR), four non-responders (NR), and four end-of-treatment responders (ETR). cDNA was synthesized, the NS5A region was amplified and the fragments obtained were cloned. Fifteen clones from each patient were sequenced with eight primers, generating 179 contigs. Results Higher values for substitution (either synonymous or non-synonymous) and for distance were found in the SVR group. However, the NR group showed relatively more non-synonymous mutations than the other groups, owing to the higher values of dN/dS in complete NS5A and most specific regions. Overall, NS5A protein is undergoing purifying selection, since all dN/dS ratios values are below 0.5. Conclusions Our study provides an overview of the genetic variability of complete NS5A protein in HCV genotype 3a.

2010-01-01

47

Genetic diversity among Bolivian arenaviruses.  

PubMed

Machupo virus and Chapare virus are members of the Tacaribe serocomplex (virus family Arenaviridae) and etiological agents of hemorrhagic fever in humans in Bolivia. The nucleotide sequences of the complete Z genes, a large fragment of the RNA-dependent RNA polymerase genes, the complete glycoprotein precursor genes, and the complete nucleocapsid protein genes of 8 strains of Machupo virus were determined to increase our knowledge of the genetic diversity among the Bolivian arenaviruses. The results of analyses of the predicted amino acid sequences of the glycoproteins of the Machupo virus strains and Chapare virus strain 200001071 indicated that immune plasma from hemorrhagic fever cases caused by Machupo virus may prove beneficial in the treatment of Bolivian hemorrhagic fever but not hemorrhagic fever caused by Chapare virus. PMID:19041349

Cajimat, Maria N B; Milazzo, Mary Louise; Rollin, Pierre E; Nichol, Stuart T; Bowen, Michael D; Ksiazek, Thomas G; Fulhorst, Charles F

2008-12-19

48

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

49

Management increases genetic diversity of honey bees via admixture.  

PubMed

The process of domestication often brings about profound changes in levels of genetic variation in animals and plants. The honey bee, Apis mellifera, has been managed by humans for centuries for both honey and wax production and crop pollination. Human management and selective breeding are believed to have caused reductions in genetic diversity in honey bee populations, thereby contributing to the global declines threatening this ecologically and economically important insect. However, previous studies supporting this claim mostly relied on population genetic comparisons of European and African (or Africanized) honey bee races; such conclusions require reassessment given recent evidence demonstrating that the honey bee originated in Africa and colonized Europe via two independent expansions. We sampled honey bee workers from two managed populations in North America and Europe as well as several old-world progenitor populations in Africa, East and West Europe. Managed bees had highly introgressed genomes representing admixture between East and West European progenitor populations. We found that managed honey bees actually have higher levels of genetic diversity compared with their progenitors in East and West Europe, providing an unusual example whereby human management increases genetic diversity by promoting admixture. The relationship between genetic diversity and honey bee declines is tenuous given that managed bees have more genetic diversity than their progenitors and many viable domesticated animals. PMID:22564213

Harpur, Brock A; Minaei, Shermineh; Kent, Clement F; Zayed, Amro

2012-05-05

50

How does ecological disturbance influence genetic diversity?  

PubMed

Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major driver that shapes patterns of genetic diversity in many natural populations. We outline how disturbance influences genetic diversity through changes in both selective processes and demographically driven, selectively neutral processes. Our review highlights the opportunities and challenges presented by genetic approaches, such as landscape genomics, for better understanding and predicting the demographic and evolutionary responses of natural populations to disturbance. Developing this understanding is now critical because disturbance regimes are changing rapidly in a human-modified world. PMID:24054910

Banks, Sam C; Cary, Geoffrey J; Smith, Annabel L; Davies, Ian D; Driscoll, Don A; Gill, A Malcolm; Lindenmayer, David B; Peakall, Rod

2013-09-19

51

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

2010-10-06

52

GENETIC DIVERSITY OF CLETHRIONOMYS GLAREOLUS POPULATIONS FROM HIGHLY CONTAMINATED SITES IN THE CHORNOBYL REGION, UKRAINE  

Microsoft Academic Search

At radioactive sites, at least two mechanisms may affect the genetic diversity of populations of a given species. Increased mutation rates due to radiation exposure may increase the amount of genetic diversity in a population. Alternatively, population bottlenecks exacerbated by environmental degradation may lead to a reduction of diversity. The relationship between these two contradictory forces is complex. To explore

Cole W. Matson; Brenda E. Rodgers; Ronald K. Chesser; Robert J. Baker

2000-01-01

53

Does genetic diversity reduce sibling competition?  

PubMed

An enduring hypothesis for the proximal benefits of sex is that recombination increases the genetic variation among offspring and that this genetic variation increases offspring performance. A corollary of this hypothesis is that mothers that mate multiply increase genetic variation within a clutch and gain benefits due to genetic diversity alone. Many studies have demonstrated that multiple mating can increase offspring performance, but most attribute this increase to sexual selection and the role of genetic diversity has received less attention. Here, we used a breeding design to generate populations of full-siblings, half-siblings, and unrelated individuals of the solitary ascidian Ciona intestinalis. Importantly, we preclude the potentially confounding influences of maternal effects and sexual selection. We found that individuals in populations with greater genetic diversity had greater performance (metamorphic success, postmetamorphic survival, and postmetamorphic size) than individuals in populations with lower genetic diversity. Furthermore, we show that by mating with multiple males and thereby increasing genetic variation within a single clutch of offspring, females gain indirect fitness benefits in the absence of mate-choice. Our results show that when siblings are likely to interact, genetic variation among individuals can decrease competition for resources and generate substantial fitness benefits within a single generation. PMID:22220867

Aguirre, J David; Marshall, Dustin J

2011-08-13

54

Bovine Genetic Diversity Revealed By mtDNA Sequence Variation  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

55

Natural hazards and genetic diversity in rice  

Microsoft Academic Search

Rice crop diversity hasdecreased dramatically in the recent past.Understanding the causes that underlie theevident genetic erosion is critical for thefood security of subsistence rice farmers andbiodiversity. Our study shows that farmers inthe northeastern Philippines had a markedreduction in rice diversity from 1996 to 1998.The ultimate causes were a drought resultingfrom the El Niño phenomenon in 1997 andflooding due to two

Stephen R. Morin; Marlon Calibo; Marilyn Garcia-Belen; Jean-Louis Pham; Florencia Palis

2002-01-01

56

Genetic Diversity of Neisseria gonorrhoeae Housekeeping Genes  

Microsoft Academic Search

Molecular typing of Neisseria gonorrhoeae strains is an important tool for epidemiological studies of gono- coccal infection and transmission. The recently developed multilocus sequence typing (MLST) method is based on the genetic variation among housekeeping genes. As a preliminary investigation for the development of such a method, we characterized the genetic diversity at 18 gonococcal housekeeping gene loci. Approximately 17,500

Raphael P. Viscidi; James C. Demma

2003-01-01

57

Genetic diversity of Cypripedium calceolus in Poland  

Microsoft Academic Search

In this work we assessed the genetic diversity of 32 C. calceolus populations from Poland. Mean genetic diversity was moderate (P = 36.4%, A = 1.58, H\\u000a O = 0.143, F\\u000a IS = 0.059), and seven geographic regions did not differ significantly in their levels of polymorphism (p > 0.05), although allele frequencies varied greatly. Only four unique alleles were found, at three sites in southern and\\u000a southeastern Poland. Genetic (P,

Emilia Brzosko; Ada Wróblewska; Izabela Ta?a?aj; Edyta Wasilewska

2011-01-01

58

Neglect of genetic diversity in implementation of the Convention on ...  

Treesearch

Description: Genetic diversity is the foundation for all biological diversity; the persistence ... World leaders have agreed on the conservation of genetic diversity as an ... This article was written and prepared by U.S. Government employees on  ...

59

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.

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

2012-01-01

60

Genetic diversity and genetic vulnerability—an appraisal  

Microsoft Academic Search

Summary  \\u000a \\u000a \\u000a \\u000a 1. \\u000a \\u000a Plant germplasm is among the most essential of the world’s natural resources. Its conservation merits far greater attention\\u000a than it is now receiving.\\u000a \\u000a \\u000a \\u000a \\u000a 2. \\u000a \\u000a Total genetic diversity does not provide insurance against genetic vulnerability. To be of use to the breeder, sources of\\u000a genetic diversity must include useful alleles not present in elite populations that carry resistance to

William L. Brown

1983-01-01

61

Genetic diversity of a Coffea Germplasm Collection assessed by RAPD markers  

Microsoft Academic Search

Genetic diversity and relationships within and among nine species of Coffea, one species of Psilanthus and the Piatã hybrid from the Coffee Germplasm Collection of Instituto Agronômico de Campinas (IAC), Brazil were assessed\\u000a using RAPD markers. Genetic diversity and relationships were evaluated by proportion of polymorphic loci (P), Shannon’s genetic index (H? and G?ST) and clustering analysis. The overall RAPD

Milene Silvestrini; Mirian P. Maluf; Maria B. Silvarolla; Oliveiro Guerreiro-Filho; Herculano P. Medina-Filho; Marina M. T. Vanini; Adalgisa S. Oliveira; Cristiana de Gaspari-Pezzopane; Luiz C. Fazuoli

2008-01-01

62

Nephronophthisis: A Genetically Diverse Ciliopathy  

PubMed Central

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

Simms, Roslyn J.; Hynes, Ann Marie; Eley, Lorraine; Sayer, John A.

2011-01-01

63

Genetic diversity analysis of common beans based on molecular markers.  

PubMed

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

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

2011-10-01

64

Genetic diversity analysis of common beans based on molecular markers  

PubMed Central

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

Gill-Langarica, Homar R.; Muruaga-Martinez, Jose S.; Vargas-Vazquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Perez, Netzahualcoyotl

2011-01-01

65

Genetic diversity of canine olfactory receptors  

Microsoft Academic Search

BACKGROUND: Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. RESULTS: We sequenced 109 OR genes considered

Stéphanie Robin; Sandrine Tacher; Maud Rimbault; Amaury Vaysse; Stéphane Dréano; Catherine André; Christophe Hitte; Francis Galibert

2009-01-01

66

Economic and biological aspects of genetic diversity  

Microsoft Academic Search

This article examines some of the characteristics of biological diversity and the appropriateness of the standard economic model in developing policies to protect genetic resources. It is argued that the assumptions of the standard model of perfect competition, including perfect information, reversibility, the emphasis on marginal analysis, and the appropriateness of discounting the future, place severe limitations on the usefulness

John M. Gowdy

1993-01-01

67

Genetic diversity and genetic differentiation of natural Pinus koraiensis population  

Microsoft Academic Search

Genetic diversities and genetic differentiations of the four Pinus koraiensis populations (Gaofeng Forestry Farm at Tangwanghe in Yichun City, Erdaobaihe Town in the Changbai Mountains, Shengshan Forestry\\u000a Farm in Heihe City, in China, and the suburb of Vladivostok City in Russia) were analyzed by using ISSR-PCR technique. The\\u000a results of 15 primers amplification showed that the ratio of polymorphic site

Fu-juan Feng; Shi-jie Han; Hong-mei Wang

2006-01-01

68

Genetic diversity of Rhodopirellula strains.  

PubMed

Rhodopirellula baltica SH1(T) is a marine planctomycete with 7,325 genes in its genome. Ten strains of the genus Rhodopirellula were studied in whole genome microarray experiments to assess the extent of their genetic relatedness to R. baltica SH1(T). DNA of strains which were previously affiliated with the species R. baltica (OTU A) hybridized with 3,645-5,728 genes of the type strain on the microarray. Strains SH398 and 6C (OTU B), representing a closely related species with an average nucleotide identity of 88 %, showed less hybridization signals: 1,816 and 3,302 genes gave a hybridization signal, respectively. Comparative genomics of eight permanent draft genomes revealed the presence of over 4,000 proteins common in R. baltica SH1(T) and strains of OTU A or B. The genus Rhodopirellula is characterized by large genomes, with over 7,000 genes per genome and a core genome of around 3000 genes. Individual Rhodopirellula strains have a large portion of strain-specific genes. PMID:23975513

Frank, Carsten S; Klockow, Christine; Richter, Michael; Glöckner, Frank Oliver; Harder, Jens

2013-08-23

69

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

PubMed

The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, that is, ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesised to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies. PMID:23006492

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

2012-09-25

70

Genetic diversity increases population productivity in a sessile marine invertebrate.  

PubMed

Reductions in genetic diversity can have widespread ecological consequences: populations with higher genetic diversity are more stable, productive and resistant to disturbance or disease than populations with lower genetic diversity. These ecological effects of genetic diversity differ from the more familiar evolutionary consequences of depleting genetic diversity, because ecological effects manifest within a single generation. If common, genetic diversity effects have the potential to change the way we view and manage populations, but our understanding of these effects is far from complete, and the role of genetic diversity in sexually reproducing animals remains unclear. Here, we examined the effects of genetic diversity in a sexually reproducing marine invertebrate in the field. We manipulated the genetic diversity of experimental populations and then measured individual survival, growth, and fecundity, as well as the size of offspring produced by individuals in high and low genetic diversity populations. Overall, we found greater genetic diversity increased performance across all metrics, and that complementarity effects drove the increased productivity of our high-diversity populations. Our results show that differences in genetic diversity among populations can have pervasive effects on population productivity within remarkably short periods of time. PMID:22764499

Aguirre, J David; Marshall, Dustin J

2012-05-01

71

Genetic diversity and geographical distribution of indigenous soybean-nodulating Bradyrhizobia in the United States  

Technology Transfer Automated Retrieval System (TEKTRAN)

The relationship of indigenous soybean-nodulating bradyrhizobial genetic diversity and geographical distribution in the United States of America (USA) were investigated using soil isolates from eight states (Michigan, Ohio, Kentucky, North Carolina, Alabama, Georgia, Florida and Louisiana) with thre...

72

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

PubMed Central

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

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

2010-01-01

73

Mapping human genetic diversity in Asia.  

PubMed

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations. PMID:20007900

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

2009-12-11

74

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

75

GENETIC DIVERSITY AND POPULATION STRUCTURE OF TEOSINTE  

Technology Transfer Automated Retrieval System (TEKTRAN)

The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics, evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships between species and subspecific taxa were largely consistent w...

76

Genetic diversity of Coccidioides posadasii from Brazil.  

PubMed

Studies of the genetic variation within populations of Coccidioides posadasii are scarce, especially for those recovered from South America. Understanding the distribution of genotypes among populations is important for epidemiological surveillance. This study evaluated the genetic diversity of 18 Brazilian strains of C. posadasii through the sequencing of the 18-28S region of nuclear rDNA, as well as through RAPD and M13-PCR fingerprinting techniques. The sequences obtained were compared to Coccidioides spp. previously deposited in GenBank. The MEGA5 program was used to perform phylogenetic analyses. Within the C. posadasii clade, a single cluster was observed, containing seven isolates from Ceará, which presented a single nucleotide polymorphism. These isolates were from the same geographical area. The strains of C. posadasii showed a lower rate of genetic diversity in the ITS1 and ITS2 regions. The results of M13 and RAPD-PCR fingerprinting indicated a similar electrophoretic profile. No differences between clinical and environmental isolates were detected. This was the first study assessing the genetic variability of a larger number of C. posadasii isolates from Brazil. PMID:23167705

Brilhante, Raimunda Sâmia Nogueira; de Lima, Rita Amanda Chaves; Ribeiro, Joyce Fonteles; de Camargo, Zoilo Pires; Castelo-Branco, Débora de Souza Collares Maia; Grangeiro, Thalles Barbosa; Cordeiro, Rossana de Aguiar; Gadelha Rocha, Marcos Fábio; Sidrim, José Júlio Costa

2012-11-21

77

Genetic Diversity in Honey Bee Colonies Enhances Productivity and Fitness  

Microsoft Academic Search

Honey bee queens mate with many males, creating numerous patrilines within colonies that are genetically distinct. The effects of genetic diversity on colony productivity and long-term fitness are unknown. We show that swarms from genetically diverse colonies (15 patrilines per colony) founded new colonies faster than swarms from genetically uniform colonies (1 patriline per colony). Accumulated differences in foraging rates,

Heather R. Mattila; Thomas D. Seeley

2007-01-01

78

Attitudes about Genetics in Underserved, Culturally Diverse Populations  

Microsoft Academic Search

Objective: New medical discoveries regarding genetic susceptibility to common chronic diseases, and the decoding of the human genome have increased public attention to genetics. What information is understood and what attitudes exist towards genetics and genetic research have not been well examined in underserved, culturally diverse communities. Methods: To better understand attitudes and beliefs towards genetics and genetic testing in

Diana S. Catz; Nancy S. Green; Jonathan N. Tobin; Michele A. Lloyd-Puryear; Penny Kyler; Ann Umemoto; Jennifer Cernoch; Roxane Brown; Fredericka Wolman

2005-01-01

79

Analysis of genetic diversity of Lactarius hatsudake in south China.  

PubMed

Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L. hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the F(ST) value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent. PMID:21815833

He, Li; Liang, Guo; Guoying, Zhou; Jun-ang, Liu

2011-08-04

80

Genetic diversity and population structure of Capsicum baccatum genetic resources  

Microsoft Academic Search

Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited\\u000a for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species’ molecular diversity and population structure in the South American\\u000a gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic

Elena Albrecht; Dapeng Zhang; Robert A. Saftner; John R. Stommel

81

Genetic diversity and environmental associations of sacsaoul ( Haloxylon ammodendron)  

NASA Astrophysics Data System (ADS)

Random amplified polymorphic DNA (RAPD) markers were used to assess levels and patterns of genetic diversity in H. ammodendron (Chenopodiaceae). A total of 117 plants from 6 subpopulations on oasis-desert ecotone was analyzed by 16 arbitrarily chosen primers resulting in highly reproducible RAPD bands. The analysis of molecular variance (AMOVA) with distances among individuals showed that most of the variation (74%) occurred among individuals within subpopulations, which is expected for a crossing organism, and 26% of variation among subpopulations. Estimates of Shannon index and Nei"s index from allele frequencies corroborated AMOVA partitioning in H. ammodendron. UPGMA cluster analyses, based on genetic distance, do not revealed grouping of some geographically proximate populations. This is the first report of the partitioning of genetic variability within and between subpopulations of H. ammodendron and provides important baseline data for optimizing sampling strategies and for conserving the genetic resources of this species. The Percentage of polymorphic loci was as high as 96%, presumably being response to oasis-desert ecotone. There were gene flows (Nm=5.38 individuals/generation), based on gene differentiation coefficient (GST was 0.1567) between subpopulations, and strong habitat selection override the gene flow to maintain the subpopulation differentiation. Correlation analyses showed that there was significant relationship between genetic diversity and soil CL ion.

Zhang, Linjing; Zhao, Guifang; Yue, Ming; Pan, Xiaoling

2003-07-01

82

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

PubMed

The relationship between genetic diversity and species diversity provides insights into biogeography and historic patterns of evolution and is critical for developing contemporary strategies for biodiversity conservation. Although concordant large-scale clines in genetic and species diversity have been described for terrestrial organisms, whether these parameters co-vary in marine species remains largely unknown. We examined patterns of genetic diversity for 11 coral reef fish species sampled at three locations across the Pacific Ocean species diversity gradient (Australia: ?1600 species; New Caledonia: ?1400 species; French Polynesia: ?800 species). Combined genetic diversity for all 11 species paralleled the decline in species diversity from West to East, with French Polynesia exhibiting lowest total haplotype and nucleotide diversities. Haplotype diversity consistently declined toward French Polynesia in all and nucleotide diversity in the majority of species. The French Polynesian population of most species also exhibited significant genetic differentiation from populations in the West Pacific. A number of factors may have contributed to the general positive correlation between genetic and species diversity, including location and time of species origin, vicariance events, reduced gene flow with increasing isolation, and decreasing habitat area from West to East. However, isolation and habitat area, resulting in reduced population size, are likely to be the most influential. PMID:23206145

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

2012-08-16

83

Aggressiveness is associated with genetic diversity in landlocked salmon (Salmo salar).  

PubMed

The amount of intraindividual genetic variation has often been found to have profound effects on life history traits. However, studies concerning the relationship between behaviour and genetic diversity are scarce. Aggressiveness is an important component of competitive ability in juvenile salmonids affecting their later performance and survival. In this study, we used an experimental approach to test the prediction that juveniles with low estimated genetic diversity should be less aggressive than juveniles with high estimated genetic diversity in fry from a highly endangered population of land-locked salmon (Salmo salar). This was achieved by using a method enabling the accurate estimation of offspring genetic diversity based on parental microsatellite genotype data. This allowed us to create two groups of offspring expected to have high or low genetic diversity in which aggressive behaviour could be compared. Salmon fry with low estimated genetic diversity were significantly less aggressive than fry with high estimated genetic diversity. Closer analysis of the data suggested that this difference was due to differences in more costly acts of aggression. Our result may reflect a direct effect of genetic variation on a fitness-related trait; however, we cannot rule out an alternative explanation of allele-specific phenotype matching, where lowered aggression is expressed towards genetically more similar individuals. PMID:12919477

Tiira, Katriina; Laurila, Anssi; Peuhkuri, Nina; Piironen, Jorma; Ranta, Esa; Primmer, Craig R

2003-09-01

84

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

85

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

Microsoft Academic Search

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary\\u000a with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes\\u000a correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence\\u000a in central stonerollers (Campostoma anomalum)

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

86

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

87

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

PubMed

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. PMID:21833642

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

2011-07-22

88

Workforce Diversity in Small Manufacturing Firms: The Complex Relationship Between Workforce Diversity and Firm Performance  

Microsoft Academic Search

Much of the literature on workforce diversity suggests that a positive relationship exists between having a diverse workforce and the effectiveness of the organization. However, little empirical evidence exists to support these claims. This study examines the relationship between workforce diversity in small manufacturing firms and various performance measures. While the data suggest that a relationship may exist, the results

Donald E. Gudmundson; Linda S. Hartenian

89

Genetic diversity and maternal origin of Bangladeshi chicken.  

PubMed

Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (?ST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity. PMID:23640100

Bhuiyan, M S A; Chen, Shanyuan; Faruque, S; Bhuiyan, A K F H; Beja-Pereira, Albano

2013-05-03

90

Genetic diversity of Ehrlichia canis in Brazil.  

PubMed

Canine monocytic ehrlichiosis is a highly prevalent disease in Brazil, where the genetic diversity of Ehrlichia canis remains undefined. In this study, we used the TRP36 gene to examine the genetic diversity of E. canis strains from naturally infected dogs residing in five distinct geographic regions in Brazil. E. canis DNA was detected in 82/126 (65%) dogs by dsb-specific PCR and E. canis was isolated in cell culture from 13 dogs. Sequences obtained from dsb genes amplified from the isolates were identical to the US E. canis strain. An extended molecular characterization based on the TRP36 gene identified two major genogroups based on differences among eight isolates. Isolates with tandem repeat amino acid sequence (TEDSVSAPA) identical to the previously reported TRP36 sequence were found in the midwest, northeast and southeast regions of Brazil, and classified into the US genogroup. A novel Brazilian genotype with a different tandem repeat sequence (ASVVPEAE) was also identified in midwest, northern and southern regions. Similarity in the N-terminal sequence of a US genogroup member with the Brazilian genogroup suggested that genomic recombination between the two genogroups may have occurred. Other subtypes within the Brazilian genogroup were also identified using C-terminal amino acid divergence. We identified two distinct major Brazilian genogroups and several subtypes based on analysis of TRP36, and such information will be useful for further genotyping and possible associations with disease severity, understanding of the genetic and antigenic variability of E. canis, and for developing strain-specific vaccines and diagnostic methods based on TRP36. PMID:23490559

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

2013-02-27

91

GENETIC DIVERSITY IN CROP IMPROVEMENT: THE SOYBEAN EXPERIENCE  

Technology Transfer Automated Retrieval System (TEKTRAN)

Crop diversity is essential to sustainable food production. Japan is a historical center of diversity for soybean (possibly introduced ca. 0 A.D.) but diversity of modern Japanese cultivars is not well characterized. The objectives of this study were to quantify genetic diversity of Japanese culti...

92

Relationships among Early European Maize Inbreds: IV. Genetic Diversity Revealed with AFLP Markers and Comparison with RFLP, RAPD, and Pedigree Data  

Microsoft Academic Search

data ranged between 0.38 and 0.77 between unrelated ( f 5 0) pairs of lines. All flint and dent inbreds showed a smaller mean GS to lines rate estimation of genetic similarity by coancestry re- from the other heterotic group than to unrelated lines from the same quires reliable and detailed pedigree records. However, heterotic group. For lines of mixed

Thomas Lubberstedt; Albrecht E. Melchinger; Marnik Vuylsteke; Martin Kuiper

93

Managing biological and genetic diversity in tropical agroforestry  

Microsoft Academic Search

The issues of biological and genetic diversity management in agroforestry are extremely complex. This paper focuses on genetic\\u000a diversity management and its implications for sustainable agroforestry systems in the tropics, and presents an analysis of\\u000a the role and importance of inter- and intra-specific diversity in agroforestry. Diversity within and between tree species\\u000a in traditional agroforestry systems and modern agroforestry technologies

K. Atta-Krah; R. Kindt; J. N. Skilton; W. Amaral

2004-01-01

94

Restoration of coral populations in light of genetic diversity estimates  

PubMed Central

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.

Porto, I.; Zubillaga, A. L.

2012-01-01

95

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

96

Genetic diversity in honey bee colonies enhances productivity and fitness.  

PubMed

Honey bee queens mate with many males, creating numerous patrilines within colonies that are genetically distinct. The effects of genetic diversity on colony productivity and long-term fitness are unknown. We show that swarms from genetically diverse colonies (15 patrilines per colony) founded new colonies faster than swarms from genetically uniform colonies (1 patriline per colony). Accumulated differences in foraging rates, food storage, and population growth led to impressive boosts in the fitness (i.e., drone production and winter survival) of genetically diverse colonies. These results further our understanding of the origins of polyandry in honey bees and its benefits for colony performance. PMID:17641199

Mattila, Heather R; Seeley, Thomas D

2007-07-20

97

Does genetic diversity limit disease spread in natural host populations?  

PubMed Central

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

King, K C; Lively, C M

2012-01-01

98

Genetic diversity and population structure of American Red Angus cattle.  

PubMed

The objective of this study was to characterize the population structure and genetic diversity of registered American Red Angus cattle. Inbreeding and average relationship coefficients, effective population size, effective number of founders, and effective number of herds supplying grandparents to the population were calculated from the recorded pedigree. Inbreeding in 1960 was 10.7% and decreased until 1974 at a rate of 0.2% per year, whereas in 1975 inbreeding was 3.2% and increased until 2005 at a rate of 0.02% per year. The numerator relationship coefficients of the 10 individual paternal grandsires (PGS; sires of sires), paternal granddams (PGD; dams of sires), maternal grandsires (MGS; sires of dams), and maternal granddams (MGD; dams of dams) that had the greatest number of registered grandprogeny, with all other registered animals, increased with their birth year from 1960 on. Average numerator relationships of these with all other PGS, PGD, MGS, MGD, bulls, and sires were greater for paternal (PGS, PGD) than maternal (MGS, MGD) pathways. The effective population size was 445, with 649 effective founders. The effective numbers of herds supplying PGS, PGD, MGS, and MGD were 435, 369, 453, and 459, respectively. Inbreeding is at a low level and the effective population size is large. The effective number of founders and effective number of herds supplying grandparents is small in relation to the total number of animals and herds, indicating the disproportionate influence of a few founders and herds on the genetics of the breed. The calculated parameters indicate satisfactory genetic diversity in American Red Angus cattle. PMID:19783699

Márquez, G C; Speidel, S E; Enns, R M; Garrick, D J

2009-09-25

99

Genetic Diversity among Clinical Isolates of Candida glabrata Analyzed by Randomly Amplified Polymorphic DNA and Multilocus Enzyme Electrophoresis Analyses  

PubMed Central

The genetic diversity of 47 clinical and reference strains of Candida glabrata from several geographical origins and diverse clinical disorders, with different antifungal susceptibilities, as well as their genetic relationships were studied through multilocus enzyme electrophoresis (MLEE) and randomly amplified polymorphic DNA (RAPD) techniques. The genetic diversity estimated for 11 MLEE loci measured as average heterozygosity (h) was 0.055. A high level of genetic relatedness among isolates was established by cluster analysis. Forty-nine RAPD markers were analyzed, and the average genetic diversity among isolates, estimated by Shannon's index (Ho), was 0.372. The ?ST values estimated through an analysis of molecular variance to assess genetic differentiation among isolates revealed no genetic differentiation among them. Our results revealed very low genetic diversity among isolates, a lack of differentiation, and no association with their geographic origin and the clinical characteristics.

Boldo, Xavier M.; Villa-Tanaca, Lourdes; Zuniga, Gerardo; Hernandez-Rodriguez, Cesar

2003-01-01

100

Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond, and its relationships with agronomic traits  

Microsoft Academic Search

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and\\u000a molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information\\u000a contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using\\u000a GS estimated from AFLP fingerprints and molecular characterization; and

Karim Sorkheh; Behrouz Shiran; T. M. Gradziel; B. K. Epperson; Pedro Martínez-Gómez; E. Asadi

2007-01-01

101

Genetic diversity enhances restoration success by augmenting ecosystem services.  

PubMed

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

2012-06-25

102

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.

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

2012-01-01

103

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

PubMed Central

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.

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

2012-01-01

104

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

2012-07-24

105

Molecular genetics of human pigmentation diversity.  

PubMed

The genetic basis underlying normal variation in the pigmentary traits of skin, hair and eye colour has been the subject of intense research directed at understanding the diversity seen both between and within human populations. A combination of approaches have been used including comparative genomics of candidate genes and the identification of regions of the human genome under positive selection, together with genome-wide and specific allele association studies. Independent selection for different pigmentation gene sets has been found between Asian, European and African populations. Several genome-wide association studies for pigmentation have now been conducted and identified single nucleotide polymorphism (SNP) markers in known, TYR, TYRP1, OCA2, SLC45A2, SLC24A5, MC1R, ASIP, KITLG and previously unknown SLC24A4, IRF4, TPCN2, candidate genes. The contribution of SNP polymorphisms present in populations from South Asia have been tested and alleles found at TYR, SLC45A2 and SLC24A5 can largely account for differences between those of darkest and lightest skin reflectance using a simple additive model. Skin and hair colour associations in Europeans are found within a range of pigmentation gene alleles, whereas blue-brown eye colour can be explained by a single SNP proposed to regulate OCA2 expression. Functional testing of variant alleles has begun to connect phenotype correlations with biological differences. Variant MC1R alleles show direct correlations between the biochemical signalling properties of the encoded receptor and the red-hair fair skin pigmentation phenotype. Direct testing of a range of clonal melanocyte cultures derived from donor skin tissue characterized for three causal SNPs within SLC45A2, SLC24A5 and OCA2 has assessed their impact on melanin content and tyrosinase enzyme activity. From a culmination of genetic and functional studies, it is apparent that a number of genes impacting melanosome biogenesis or the melanin biosynthetic pathway are candidates to explain the diversity seen in human pigmentation. PMID:19297406

Sturm, Richard A

2009-04-15

106

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

107

Beauveria bassiana: Quercetinase production and genetic diversity.  

PubMed

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

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

2011-03-01

108

Genetic Diversity in Cultivated Groundnut Based on SSR Markers  

Microsoft Academic Search

Peanut (Arachis hypogaea L.) is an important source crop for edible oil and protein. It is important to identify the genetic diversity of peanut genetic resources for cultivar development and evaluation of peanut accessions. Thirty-four SSR markers were used to assess the genetic variation of four sets of twenty-four accessions each from the four botanical varieties of the cultivated peanut.

Ronghua Tang; Guoqing Gao; Liangqiong He; Zhuqiang Han; Shihua Shan; Ruichun Zhong; Cuiqiu Zhou; Jing Jiang; Yangrui Li; Weijian Zhuang

2007-01-01

109

Relationship of Genetic Variation to Population Size in Wildlife  

Microsoft Academic Search

Genetic diversity is one of three levels of biological diversity requiring conservation. Genetic theory predicts that levels of genetic variation should increase with effective population size. Sould (19 76) compiled the first convincing evidence that levels of genetic variation in wildlife were related to population size, but this issue remains controversial. The hypothesis that genetic variation is related to population

Richard Frankham

1996-01-01

110

Connectivity, scale-dependence, and the productivity-diversity relationship  

Microsoft Academic Search

We surveyed freshwater ponds (localities) nested within watersheds (regions) to evaluate the relationship between productivity and animal species richness at different spatial scales. In watersheds where the ponds were relatively distant from one another (likely reducing the level of interpond dispersal of many organisms), we found a scale- dependent productivity-diversity relationship; at local scales (among ponds), diversity was a hump-shaped

Jonathan M. Chase; Wade A. Ryberg

2004-01-01

111

The Green Revolution and wheat genetic diversity: Some unfounded assumptions  

Microsoft Academic Search

Two propositions have become common assumptions in the development literature: 1.(a) the Green Revolution caused genetic erosion, and2.(b) the Green Revolution increased genetic vulnerability. With regard to the first proposition, no causal relationship between the Green Revolution and genetic erosion can be established for bread wheat given the difficulties in measuring genetic erosion and of demonstrating causality. The pattern of

Melinda Smale

1997-01-01

112

Limited intra-genetic diversity in Dientamoeba fragilis housekeeping genes.  

PubMed

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

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

2013-05-13

113

Sexual selection and individual genetic diversity in a songbird.  

PubMed Central

Here, we report for the first time, to our knowledge, a strong correlation between a measure of individual genetic diversity and song complexity, a sexually selected male trait in sedge warblers, Acrocephalus schoenobaenus. We also find that females prefer to mate with males who will maximize this diversity in individual progeny. The genetic diversity of each offspring is further increased by means of nonrandom fertilization, as we also show that the fertilizing sperm contains a haplotype more genetically distant to that of the egg than expected by chance. These findings suggest that species' mating preferences may be subject to fine tuning aimed at increasing offspring viability through increased genetic diversity. This includes external and internal mechanisms of selection, even within the ejaculate of a single male.

Marshall, Rupert C; Buchanan, Katherine L; Catchpole, Clive K

2003-01-01

114

Limited Genetic Diversity of Recent Invasive Isolates of Non-Serotype b Encapsulated Haemophilus influenzae  

PubMed Central

Invasive infections caused by non-type b encapsulated Haemophilus influenzae have increased in frequency in the last decade. This change prompted us to characterize the genetic relationships of 48 recently isolated invasive H. influenzae type a (Hia), e (Hie), and f (Hif) strains by comparison of restriction digest patterns (RDPs). Recent Hia isolates exhibited moderate genetic diversity, with the majority segregating into two major clonotypes. Recent Hie and, especially, Hif strains displayed considerably restricted genetic diversity. In particular, all but one Hif strain segregated into a single clonotype, and half of these isolates had identical RDPs. These results are consistent with the hypothesis that the increased incidence of disease due to non-type b encapsulated H. influenzae reflects the emergence of hypervirulent clones, especially in the case of Hif. Alternatively, it is possible that non-type b encapsulated H. influenzae strains have limited overall genetic diversity.

Omikunle, Adebomi; Takahashi, Shinji; Ogilvie, Chrishana L.; Wang, Yan; Rodriguez, Carina A.; St. Geme, Joseph W.; Adderson, Elisabeth E.

2002-01-01

115

Construction of fingerprinting and genetic diversity of mulberry cultivars in China by ISSR markers.  

PubMed

The ISSR fingerprintings of 24 mulberry cultivars were constructed. Totally 80 bands were produced using 17 primers selected from 20 primers. Of them, 40 bands showed polymorphism. From the bands amplified, there were three independent ways to identify the mulberry varieties, such as unique ISSR markers, unique band patterns and a combination of the band patterns provided by different primers. ISSRs were very effective in differentiating the mulberry varieties. The mean genetic similarity coefficient, the mean Nei's gene diversity (h), and the mean Shannon's Information index (I) of mulberry cultivars were 0.8731, 0.1210, and 0.1942, respectively. This suggests that the genetic diversity of mulberry cultivars was low and the genetic base was narrow. Both UPGMA cluster and PCA (Principal Coordinates Analysis) analysis showed clear genetic relationships among the 24 mulberry cultivars. The major clusters were related to known pedigree relationships. PMID:16980132

Zhao, Wei-Guo; Miao, Xue-Xia; Zang, Bo; Zhang, Lin; Pan, Yi-Le; Huang, Yong-Ping

2006-09-01

116

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

117

Genetic diversity and selection in the maize starch pathway  

PubMed Central

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

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

2002-01-01

118

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

119

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

Microsoft Academic Search

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.

Anders Johansson; Anna Aspan; Elisabeth Bagge; Viveca Båverud; Björn E Engström; Karl-Erik Johansson

2006-01-01

120

Diversity analysis in cellular and multipopulation genetic programming  

Microsoft Academic Search

This paper presents a study that evaluates the influence of the parallel genetic programming (GP) models in maintaining diversity in a population. The parallel models used are the cellular and the multipop- ulation one. Several measures of diversity are consid- ered to gain a deeper understanding of the conditions under which the evolution of both models is successful. Three standard

Gianluigi Folino; Clara Pizzuti; Giandomenico Spezzano; Leonardo Vanneschi; Marco Tomassini

2003-01-01

121

Genetic diversity among five T4-like bacteriophages  

Microsoft Academic Search

BACKGROUND: Bacteriophages are an important repository of genetic diversity. As one of the major constituents of terrestrial biomass, they exert profound effects on the earth's ecology and microbial evolution by mediating horizontal gene transfer between bacteria and controlling their growth. Only limited genomic sequence data are currently available for phages but even this reveals an overwhelming diversity in their gene

James M Nolan; Vasiliy Petrov; Claire Bertrand; Henry M Krisch; Jim D Karam

2006-01-01

122

Genetic Diversity and Differentiation in Hedychium spicatum, a Valuable Medicinal Plant of Indian Himalaya  

Microsoft Academic Search

Hedychium spicatum, a perennial rhizomatous medicinal plant distributed in subtropical and temperate parts, is considered nearly endemic to\\u000a the Himalayan region.In this study allozyme markers were utilized to assess genetic variations and relationships among 12\\u000a distinct populations of this species from the West Himalaya of India. A high level of genetic diversity was found among the\\u000a populations. Of the 13

Arun Jugran; Indra D. Bhatt; Sandeep Rawat; Lalit Giri; Ranbeer S. Rawal; Uppeandra Dhar

123

HLA class II Genetic Diversity in Arabs and Jews of Iran  

Microsoft Academic Search

Background: Anthropological studies based on highly polymorphic HLA genes pro- vide useful information for bone marrow donor registry, forensic medicine, disease as- sociation studies, as well as designing peptide vaccines against tumors, and infectious or autoimmune diseases. Objective: This study was designed to investigate the genetic relationship of Iranian Arabs and Jews using HLA-class II genetic diversity Methods: HLA-DRB1, DQA1,

Shirin Farjadian; Abbas Ghaderi

124

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

125

Genetic diversity of local geese of varying productivity and feather color in Kars  

Microsoft Academic Search

The local geese in the transition region between the Caucasus Mountains and Anatolia have economically significant differences\\u000a in productivity and are identified by four feather colors, white, black, piebald, and yellow. This study was undertaken to\\u000a determine the genetic structure, evolutionary relationships, and genetic diversity among these birds. DNA samples were obtained\\u000a from 100 animals, and 50 random primers were

Alparslan Kadir Devrim; Necati Kaya; Aysel Guven; Buket Kocer

2007-01-01

126

Genetic Diversity of Eurycoma longifolia Inferred from Single Nucleotide Polymorphisms  

Microsoft Academic Search

Eurycoma longifolia Jack. is a treelet that grows in the forests of Southeast Asia and is widely used throughout the region because of its reported medicinal properties. Widespread harvesting of wild-grown trees has led to rapid thinning of natural populations, causing a potential decrease in genetic diversity among E. longifolia. Suitable genetic markers would be very useful for propagation and

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

2003-01-01

127

Effects of genetic impoverishment on plant community diversity  

Microsoft Academic Search

Summary 1 Established individuals removed at random from populations of 11 long-lived herbaceous species coexisting in a local area of ancient limestone pasture at Cress- brookdale in North Derbyshire were subjected to clonal propagation to produce stocks of genetically identical individuals sufficient to create 36 model communities identical in species composition but widely contrasted in genetic diversity. 2 Three levels

Rosemary E. Booth; J. Philip Grime

2003-01-01

128

Genetic diversity of Toxoplama gondii isolates from Ethiopian feral cats  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

129

Low Genetic Diversity of the Turopolje Pig Breed  

Microsoft Academic Search

Summary We have performed a genetic diversity study of the Turopolje pig breed. Microsa- tellite genotyping on ten loci recommended by International Society for Animal Genetics (ISAG) and Food and Agriculture Organization (FAO) as well as mitochondrial D-loop se- quencing were chosen as methods. Allele numbers, effective allele numbers (Ne), poly- morphism information content (PIC), observed and expected heterozygosities were

Matija Harcet; Vera Gamulin

2006-01-01

130

Glacial Refugia: Hotspots But Not Melting Pots of Genetic Diversity  

Microsoft Academic Search

Glacial refuge areas are expected to harbor a large fraction of the intraspecific biodiversity of the temperate biota. To test this hypothesis, we studied chloroplast DNA variation in 22 widespread European trees and shrubs sampled in the same forests. Most species had genetically divergent populations in Mediterranean regions, especially those with low seed dispersal abilities. However, the genetically most diverse

Rémy J. Petit; Itziar Aguinagalde; Jacques-Louis de Beaulieu; Christiane Bittkau; Simon Brewer; Rachid Cheddadi; Richard Ennos; Silvia Fineschi; Delphine Grivet; Martin Lascoux; Aparajita Mohanty; Gerhard Müller-Starck; Brigitte Demesure-Musch; Anna Palmé; Juan Pedro Martín; Sarah Rendell; Giovanni G. Vendramin

2003-01-01

131

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

132

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

PubMed

Syzygium cumini Linn. (Myrtaceae) is a medicinal tree (Jamun) used worldwide in treatment of diabetes. However, no molecular data is available on genetic polymorphism and its relationship, if any with fluoride pollution. In the present study, the genetic variability of two populations of S. cumini growing in fluoride rich soils and normal soils located in Rajasthan and Haryana regions of India, respectively was determined using random amplified polymorphic DNA (RAPD) markers. Different measures of diversity in Rajasthan populations: Shannon's index of phenotypic diversity (I) = 0.440; Nei's genetic diversity (h) = 0.292; effective number of alleles per locus (Ne) = 1.497; total species diversity (Hsp) = 0.307 and within population diversity (Hpop) = 0.158 showed high diversity in comparison to Haryana populations. Thus, it seems that Rajasthan population responds with increased genetic variation resulting possibly from new mutation that affect allele frequencies as a consequence of adaptation to contaminated environment. This may imply that the increased diversity levels may act as a buffer to combat fluoride stress. Cluster analysis and principal component analysis (PCA) results showed mixing between the populations. PMID:23360002

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

2012-07-01

133

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

134

Genetic diversity and variation among botanical varieties of old Portuguese wheat cultivars revealed by ISSR assays.  

PubMed

Inter-simple sequence repeats (ISSRs) were used for genetic diversity analyses of an Old Portuguese wheat collection. Eighteen primers produced 96.3 and 98.5% of ISSR polymorphism in bread and durum wheat cultivars, respectively. The unweighted pair group method with arithmetical averages (UPGMA) phenogram clearly split all cultivars based on their species/ploidy, reflecting a defined genetic structure. ISSRs revealed high genetic diversity at interspecific, intraspecific, and intercultivar levels. Thirty-three exclusive ISSR markers were found. Cultivars were clustered according to their botanical varieties and, in a few cases, with their homonym(s). No statistically significant differences were found between genetic diversity parameters of durum and bread wheat, probably due to high intraspecific diversity. Similar analyses were performed among botanical varieties, and their relationships were defined. Cladograms resembled UPGMA clustering. This highly genetically diverse Old wheat collection will be conserved and maintained, and it could be further used in breeding programs to widen the narrow genetic basis of modern wheat varieties and to avoid the loss of rare and unique alleles. PMID:19184405

Carvalho, Ana; Lima-Brito, José; Maçãs, Benvindo; Guedes-Pinto, Henrique

2009-01-31

135

Genetic and environmental influences on marital relationships.  

PubMed

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

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

2004-03-01

136

The relationship between diversity and productivity in selected ...  

Treesearch

... presumably because individuals engage in niche partitioning to occupy any ... Relationships between diversity and biomass productivity in two contrasting forest ... This article was written and prepared by U.S. Government employees on  ...

137

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

PubMed

We recently reported a positive association between female promiscuity and genetic diversity across passerine birds, and launched the hypothesis that female promiscuity acts as a balancing selection, pressure maintaining genetic diversity in populations (Gohli et al. ). Spurgin () questions both our analyses and interpretations. While we agree that the hypothesis needs more comprehensive empirical testing, we find his specific points of criticism unjustified. In a more general perspective, we call for a more explicit recognition of female mating preferences as mechanisms of selection in population genetics theory. PMID:24094357

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

2013-08-13

138

Genetic Diversity and Genetic Structure of an Endangered Species, Trillium tschonoskii  

Microsoft Academic Search

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (HE) within populations

Qun Li; Meng Xiao; Liang Guo; Li Wang; Lin Tang; Ying Xu; Fang Yan; Fang Chen

2005-01-01

139

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

140

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

PubMed

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

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

2013-05-01

141

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

2010-01-15

142

Genetic diversity in Hemileia vastatrix based on RAPD markers.  

PubMed

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs. PMID:16396347

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

143

Impacts of genetic bottlenecks on soybean genome diversity  

PubMed Central

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

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

2006-01-01

144

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

2013-07-03

145

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.  

PubMed

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies. PMID:16845522

Yang, Shiying; Pang, Wen; Ash, Gavin; Harper, John; Carling, Jason; Wenzl, Peter; Huttner, Eric; Zong, Xuxiao; Kilian, Andrzej

2006-07-15

146

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

2011-09-16

147

Vietnamese chickens: a gate towards Asian genetic diversity  

PubMed Central

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

2010-01-01

148

Development of molecular tools for characterization and genetic diversity analysis in Tunisian fig (Ficus carica) cultivars.  

PubMed

Fig, Ficus carica L., is a useful genetic resource for commercial cultivation. In this study, RAPD (60), ISSR (48), RAMPO (63), and SSR (34) markers were compared to detect polymorphism and to establish genetic relationships among Tunisian fig tree cultivars. The statistical procedures conducted on the combined data show considerable genetic diversity, and the tested markers discriminated all fig genotypes studied. The identification key established on the basis of SSR permitted the unambiguous discrimination of cultivars and confirmed the reliability of SSR for fingerprinting fig genotypes. The study findings are discussed in relation to the establishment of a national reference collection that will aid in the conservation of Tunisian fig resources. PMID:20628809

Chatti, Khaled; Baraket, Ghada; Ben Abdelkrim, Ahmed; Saddoud, Olfa; Mars, Messaoud; Trifi, Mokhtar; Salhi Hannachi, Amel

2010-07-14

149

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.

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

2012-01-01

150

The Host Genetic Diversity in Malaria Infection  

PubMed Central

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

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

2012-01-01

151

Genetic Diversity for Aluminum Tolerance in Sorghum  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

152

Genetic Diversity among Ancient Nordic Populations  

PubMed Central

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

Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, J?rgen

2010-01-01

153

Genetic diversity of Plasmodium vivax and Plasmodium falciparum in Honduras  

PubMed Central

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

2012-01-01

154

Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals  

Microsoft Academic Search

Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering ~3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species,

Eric Bazin; Sylvain Glémin; Nicolas Galtier

2006-01-01

155

Genetic diversity between human metapneumovirus subgroups  

Microsoft Academic Search

Complete consensus nucleotide sequences were determined for human metapneumovirus (HMPV) isolates CAN97-83 and CAN98-75, representing the two proposed genotypes or genetic subgroups of HMPV. The overall level of genome nucleotide sequence identity and aggregate proteome amino acid sequence identity between the two HMPV subgroups were 80 and 90%, respectively, similar to the respective values of 81 and 88% between the

Stéphane Biacchesi; Mario H Skiadopoulos; Guy Boivin; Christopher T Hanson; Brian R Murphy; Peter L Collins; Ursula J Buchholz

2003-01-01

156

Invasive predators deplete genetic diversity of island lizards.  

PubMed

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

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

2010-08-10

157

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.

2011-01-01

158

Genetic diversity of Actinobacillus lignieresii isolates from different hosts.  

PubMed

Genetic diversity detected by analysis of amplified fragment length polymorphisms (AFLPs) of 54 Actinobacillus 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

Kokotovic, Branko; Angen, Øystein; Bisgaard, Magne

2011-02-08

159

Landscape, population structure and genetic diversity of Stomoxys calcitrans.  

PubMed

To investigate whether different landscapes could affect genetic diversity and structure of the cosmopolitan diptera Stomoxys calcitrans, populations from Gabon and southern France were studied using dominant amplified fragment length polymorphism (AFLP) markers. Gabon is characterized by a forested closed landscape, and southern France by an open Mediterranean landscape. The genetic diversity between Gabon and France populations did not differ significantly (P > 0.05). Contrary to our expectation, this study shows a moderate level of genetic differentiation between these two distant countries (Fst = 0.0979) and a low genetic structure among Gabonese and French populations (Fst = 0.0291 and 0.0275 respectively). This result could indicate the capacities of S. calcitrans populations to sustain a high level of gene flow, despite geographic distance and isolation. PMID:19353950

Dsouli Aymes, N; Mavoungou, J F; De Stordeur, E; Duvallet, G

2009-03-01

160

Frequent coinfection reduces RNA virus population genetic diversity.  

PubMed

The masking of deleterious mutations by complementation and the reassortment of virus segments (virus sex) are expected to increase population genetic diversity among coinfecting viruses. Conversely, clonally reproducing or noncoinfecting virus populations may experience clonal interference where viral clones compete with one another, preventing selective sweeps. This dynamic reduces the efficiency of selection and increases the genetic diversity. To determine the relative influences of these forces on population genetic diversity, we evolved 6 populations of bacteriophage ?6 under conditions promoting or preventing coinfection. Following 300 generations, we isolated and partially sequenced 10 clones from each population. We found greater diversity among asexual populations than sexual populations. Moreover, sexual populations did not show greater relative fitnesses than asexual populations, implying that reduced genetic variation did not result from purifying selection. However, sexual populations were less genetically robust than asexual populations and likely more prone to the deleterious epistatic effects of mutations. As such, a neutral mutation on the asexually evolved (robust) background could be profoundly deleterious on the sexually evolved (brittle) background. This could facilitate sexual populations undergoing greater purifying selection to remove deleterious mutations, but this selection is not reflected by increases in average population fitness. Our results bolster a growing literature suggesting that RNA virus segmentation is probably not a mechanism that evolved because it provides a generalized benefit of sex. PMID:23828608

Dennehy, John J; Duffy, Siobain; O'Keefe, Kara J; Edwards, Scott V; Turner, Paul E

2013-07-04

161

Castor bean organelle genome sequencing and worldwide genetic diversity analysis.  

PubMed

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

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

2011-07-07

162

Pheochromocytomas: from genetic diversity to new paradigms.  

PubMed

Pheochromocytomas and paragangliomas are catecholamine-secreting tumors of neural crest origin caused by germline mutations in at least six distinct genes. This genetic heterogeneity has provided a rich source for both the discovery and functional characterization of new tumor-related genes. However, the genetic repertoire of these tumors is still not fully known, and current evidence points to the existence of additional pheochromocytoma susceptibility genes. Here, the unique contributions of three hereditary models of pheochromocytoma that can advance our knowledge of the disease pathogenesis are presented. The first model, loss of succinate dehydrogenase (SDH) function, illustrates how SDHB, C, or D mutations, components of the energy metabolism pathway, serve as a unique system to explore the pervasive metabolic shift of cancer cells towards glycolysis as a source of energy (also known as the Warburg effect) in contrast to the characteristic oxidative phosphorylation of normal cells. In the second model, mechanisms of tumorigenesis distinct from classical pheochromocytoma susceptibility genes are discussed in the context of a novel putative suppressor of neural crest-derived tumors, the KIF1B beta gene. Finally, NF1 loss is highlighted as a valuable study model to investigate the cell lineage selectivity of the Egln3-mediated developmental apoptotic defect of chromaffin precursor cells. Results from these studies may offer clues to understand the tissue specificity of hereditary pheochromocytoma syndromes. These distinct hereditary disease models illustrate how genetic-driven progress has the potential to narrow current gaps in our knowledge of pheochromocytoma and paraganglioma pathogenesis. PMID:19391076

Qin, Y; Buddavarapu, K; Dahia, P L M

2009-04-23

163

Genetic evolution and diversity of common carp Cyprinus carpio L  

Microsoft Academic Search

Knowledge of genetic variation and population structure of existing strains of both farmed and wild common carp Cyprinus carpio L. is absolutely necessary for any efficient fish management and\\/or conservation program. To assess genetic diversity in\\u000a common carp populations, a variety of molecular markers were analyzed. Of those, microsatellites and mitochondrial DNA were\\u000a most frequently used in the analysis of

Dimitry A. Chistiakov; Natalia V. Voronova

2009-01-01

164

Virulence and competitive ability in genetically diverse malaria infections.  

PubMed

Explaining parasite virulence is a great challenge for evolutionary biology. Intuitively, parasites that depend on their hosts for their survival should be benign to their hosts, yet many parasites cause harm. One explanation for this is that within-host competition favors virulence, with more virulent strains having a competitive advantage in genetically diverse infections. This idea, which is well supported in theory, remains untested empirically. Here we provide evidence that within-host competition does indeed select for high parasite virulence. We examine the rodent malaria Plasmodium chabaudi in laboratory mice, a parasite-host system in which virulence can be easily monitored and competing strains quantified by using strain-specific real-time PCR. As predicted, we found a strong relationship between parasite virulence and competitive ability, so that more virulent strains have a competitive advantage in mixed-strain infections. In transmission experiments, we found that the strain composition of the parasite populations in mosquitoes was directly correlated with the composition of the blood-stage parasite population. Thus, the outcome of within-host competition determined relative transmission success. Our results imply that within-host competition is a major factor driving the evolution of virulence and can explain why many parasites harm their hosts. PMID:15894623

de Roode, Jacobus C; Pansini, Riccardo; Cheesman, Sandra J; Helinski, Michelle E H; Huijben, Silvie; Wargo, Andrew R; Bell, Andrew S; Chan, Brian H K; Walliker, David; Read, Andrew F

2005-05-13

165

Virulence and competitive ability in genetically diverse malaria infections  

PubMed Central

Explaining parasite virulence is a great challenge for evolutionary biology. Intuitively, parasites that depend on their hosts for their survival should be benign to their hosts, yet many parasites cause harm. One explanation for this is that within-host competition favors virulence, with more virulent strains having a competitive advantage in genetically diverse infections. This idea, which is well supported in theory, remains untested empirically. Here we provide evidence that within-host competition does indeed select for high parasite virulence. We examine the rodent malaria Plasmodium chabaudi in laboratory mice, a parasite–host system in which virulence can be easily monitored and competing strains quantified by using strain-specific real-time PCR. As predicted, we found a strong relationship between parasite virulence and competitive ability, so that more virulent strains have a competitive advantage in mixed-strain infections. In transmission experiments, we found that the strain composition of the parasite populations in mosquitoes was directly correlated with the composition of the blood-stage parasite population. Thus, the outcome of within-host competition determined relative transmission success. Our results imply that within-host competition is a major factor driving the evolution of virulence and can explain why many parasites harm their hosts.

de Roode, Jacobus C.; Pansini, Riccardo; Cheesman, Sandra J.; Helinski, Michelle E. H.; Huijben, Silvie; Wargo, Andrew R.; Bell, Andrew S.; Chan, Brian H. K.; Walliker, David; Read, Andrew F.

2005-01-01

166

Intrinsic time dependence in the diversity-invasibility relationship.  

PubMed

Contrasting patterns in the diversity-invasibility relationship have intrigued ecologists for many years, and are now known as the "invasion paradox." Experiments usually detect negative relationships, while field surveys find them to be positive. It is widely believed that the paradox is driven by differences in spatial scale, but this is challenged by field surveys that find positive relationships at all spatial scales. If factors that determine invasion dynamics change during the invasion process, the paradox may be partially driven by differences in temporal scale. Here we used simulation (cellular automata) models to explore the generality of temporal change in the diversity-invasibility relationship. The probability of invaders colonizing an area was inversely related to the density of natives, creating a negative native-exotic correlation when invaders first arrived. Over time, native and exotic populations were both shaped by the same post-introduction processes (disturbance, dispersal, and recolonization), shifting their correlation to positive. The rate of temporal change in the diversity-invasibility relationship was mainly dependent upon the fecundity of invaders. Greater fecundity meant that invaders spread through the landscape faster and were subject to post-introduction processes sooner. We propose a unified conceptual model where the diversity-invasiblity relationship is a function of both spatial and temporal scales. PMID:23600237

Clark, Graeme F; Johnston, Emma L; Leung, Brian

2013-01-01

167

Chromatid structure: relationship between DNA content and nucleotide sequence diversity  

Microsoft Academic Search

Models of chromatid structure are based on inferences made from genetic, cytological, and cytochemical observations. An alternative approach can provide limits as to the number of identical subunits present in chromatids. This method is based on the demonstration that nucleotide sequence diversity may be estimated from the kinetics of renaturation of denatured DNA. Measurements of DNA content and renaturation rate

Charles D. Laird

1971-01-01

168

Genetic Diversity and Population Structure of Cucumber (Cucumis sativus L.)  

PubMed Central

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

Shao, Guangjin; Li, Hang; Sun, Zhanyong; Weng, Yiqun; Shang, Yi; Gu, Xingfang; Li, Xixiang; Zhu, Xiaoguo; Zhang, Jinzhe; van Treuren, Robbert; van Dooijeweert, Willem; Zhang, Zhonghua; Huang, Sanwen

2012-01-01

169

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

PubMed

Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber. PMID:23071663

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

2012-10-12

170

Genetic diversity of the wild and reared Pseudosciaena crocea  

NASA Astrophysics Data System (ADS)

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

Wang, Jun; Su, Yong-Quan; Quan, Cheng-Gan; Ding, Shao-Xiong; Zhang, Wen

2001-06-01

171

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.

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

2009-01-01

172

Genetic diversity and genetic similarities between Iranian rose species  

Microsoft Academic Search

Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified

L. Samiei; R. Naderi; A. Khalighi; A. A. Shahnejat-Bushehri; V. Mozaffarian; G. D. Esselink; S. Kazempour Osaloo; M. J. M. Smulders

2010-01-01

173

Genetic diversity and conservation in a small endangered horse population.  

PubMed

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

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

2013-05-07

174

Genetic diversity in Taro ( Colocasia esculenta Schott, Araceae) in China: An ethnobotanical and genetic approach  

Microsoft Academic Search

Taro,Colocasia esculenta (Araceae), is a widely distributed and important food crop in the humid tropics and subtropics. Relatively neglected by science,\\u000a much knowledge of genetic diversity in taro is with farmers. Taro genetic resources managed by five ethnic communities and\\u000a Han farming villages in diverse ecosystems were sampled and characterized in Yunnan Province, southwest China. This study\\u000a documented a new

Xu Jianchu; Yang Yongping; Pu Yingdong; W. G. Ayad; P. B. Eyzaguirre

2001-01-01

175

The Loss of Genetic Diversity in Sichuan Taimen as Revealed by DNA Fingerprinting  

Microsoft Academic Search

Species endangerment often derives from the “endangerment” of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during1998–1999 and obtained historical specimens from

Xue-Chang Wu

2006-01-01

176

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

Microsoft Academic Search

The frequency of polyploidy increases with latitude in the Northern Hemisphere, especially in deglaciated, recently colonized areas. The cause or causes of this pattern are largely unknown, but a greater genetic diversity of individual polyploid plants due to a doubled genome and\\/or a hybrid origin is seen as a likely factor underlying selective advantages related to life in extreme climates

PIETERNELLA C. LUTTIKHUIZEN; MARC STIFT; PETER KUPERUS; Tienderen van P. H

2007-01-01

177

A COMPARISON OF GENETIC DIVERSITY IN NORTH AMERICAN BROWN BEARS  

Microsoft Academic Search

To determine if threatened brown bear (Ursus arctos) populations of Montana and Wyoming have lower levels of genetic variation than other North American populations, we examined mitochondrial DNA (mtDNA) and nuclear microsatellite DNA diversity in 220 brown bears from 5 areas: Kodiak Island, Alaska; Kluane National Park, Canada; Eastern Slope of the Rockies (East Slope), Canada; Yellowstone ecosystem (YE), Wyoming

LISETTE WAITS; DAVID PAETKAU; CURTIS STROBECK; RICHARD H. WARD

178

Genetic diversity of noroviruses in raw and treated sewage water  

Microsoft Academic Search

Human noroviruses cause gastroenteritis in humans, leading to high virus loads in sewage. Norovirus concentrations in raw and treated sewage samples from two sewage treatment plants (STP) were studied, along with virus removal and genetic diversity. Over one year, the average norovirus concentrations in raw sewage were approximately 105 pcr detectable units (pdu) per liter compared with 103 pdu\\/l of treated sewage.

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

2005-01-01

179

Genome-Wide Reduction of Genetic Diversity in Wheat Breeding  

Microsoft Academic Search

Public concerns about crop uniformity intro- duced by modern plant breeding and genetic vulnerability to biotic and abiotic stresses have been one of the major forces driving long-term efforts in plant germplasm conservation for future food security. However, such concerns have gained little empirical support, as recent molecular diversity analyses of improved crop gene pools did not reveal much reduction

Yong-Bi Fu; Daryl J. Somers

2009-01-01

180

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.

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

2013-01-01

181

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

2013-09-09

182

Genetic diversity of Cryptosporidium spp. from Bangladeshi children.  

PubMed

The genetic diversity of Cryptosporidium spp. from infected children was characterized for the first time in Bangladesh. Seven C. hominis and C. parvum subtype families (including a new family, IIm) and 15 subtypes (including 2 new subtypes) were identified. The dominance of specific families and subtypes was different from that in other countries. PMID:21471344

Hira, Kirthi G; Mackay, Melanie R; Hempstead, Andrew D; Ahmed, Sabeena; Karim, Mohammad M; O'Connor, Roberta M; Hibberd, Patricia L; Calderwood, Stephen B; Ryan, Edward T; Khan, Wasif A; Ward, Honorine D

2011-04-06

183

GENETIC DIVERSITY IN AN ISOLATED POPULATION OF Capparis decidua  

Microsoft Academic Search

Summary Capparis decidua is a rangland plant species growing in isolated regions in Saudi Arabia. RAPD markers were used to study genetic diversity in a population present in Raudhat Khuraim and a control population. Cluster analysis showed that coefficient of similarity within Raudhat Khuraim population (84-93%) is a lot larger than between Raudhat Khuraim and the control population (77%).This indicates

A. L. Abdel-Mawgood; A. Assaeed; T. Al-Abdallatif

184

Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae).  

PubMed

Hybridisation among taxa with different ploidy levels is often associated with hybrid sterility. Clonal reproduction can stabilise these hybrids, but pervasive clonality may have a profound impact on the distribution of genetic diversity in natural populations. Here we investigate a widespread triploid taxon resulting from hybridisation between diploid Mimulus guttatus and tetraploid Mimulus luteus, two species that were introduced into the United Kingdom (UK) in the nineteenth century. This hybrid, Mimulus x robertsii, is largely sterile but capable of prolific vegetative propagation and has been recorded in the wild since 1872. We surveyed 40 Mimulus populations from localities across the UK to examine the current incidence of hybrids, and selected seventeen populations for genetic analysis using codominant markers. Cluster analyses revealed two main groups of genetically distinct individuals, corresponding to either diploid (M. guttatus) or polyploid (M. luteus and M. x robertsii) samples. Triploid hybrids were found in around 50% of sampled sites, sometimes coexisting with one of the parental species (M. guttatus). The other parent, M. luteus, was restricted to a single locality. Individual populations of M. x robertsii were genetically variable, containing multiple, highly heterozygous clones, with the majority of genetic variation distributed among- rather than within populations. Our findings demonstrate that this largely sterile, clonal taxon can preserve non-negligible amounts of genetic variation. The presence of genetically variable hybrid populations may provide the material for the continued success of asexual taxa in diverse environments. PMID:23169562

Vallejo-Marin, M; Lye, G C

2012-11-21

185

Genetic diversity within and genetic differentiation between blooms of a microalgal species.  

PubMed

The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G.?semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction. PMID:22568551

Lebret, Karen; Kritzberg, Emma S; Figueroa, Rosa; Rengefors, Karin

2012-05-09

186

Genetic diversity within and genetic differentiation between blooms of a microalgal species  

PubMed Central

The field of genetic diversity in protists, particularly phytoplankton, is under expansion. However, little is known regarding variation in genetic diversity within populations over time. The aim of our study was to investigate intrapopulation genetic diversity and genetic differentiation in the freshwater bloom-forming microalga Gonyostomum semen (Raphidophyceae). The study covered a 2-year period including all phases of the bloom. Amplified fragment length polymorphism (AFLP) was used to determine the genetic structure and diversity of the population. Our results showed a significant differentiation between samples collected during the two blooms from consecutive years. Also, an increase of gene diversity and a loss of differentiation among sampling dates were observed over time within a single bloom. The latter observations may reflect the continuous germination of cysts from the sediment. The life cycle characteristics of G. semen, particularly reproduction and recruitment, most likely explain a high proportion of the observed variation. This study highlights the importance of the life cycle for the intraspecific genetic diversity of microbial species, which alternates between sexual and asexual reproduction.

Lebret, Karen; Kritzberg, Emma S; Figueroa, Rosa; Rengefors, Karin

2012-01-01

187

Evaluation of genetic diversity and population structure of West-Central Indian cattle breeds.  

PubMed

Evaluations of genetic diversity in domestic livestock populations are necessary to implement region-specific conservation measures. We determined the genetic diversity and evolutionary relationships among eight geographically and phenotypically diverse cattle breeds indigenous to west-central India by genotyping these animals for 22 microsatellite loci. A total of 326 alleles were detected, and the expected heterozygosity ranged from 0.614 (Kenkatha) to 0.701 (Dangi). The mean number of alleles among the cattle breeds ranged from 7.182 (Khillar) to 9.409 (Gaolao). There were abundant genetic variations displayed within breeds, and the genetic differentiation was also high between the Indian cattle breeds, which displayed 15.9% of the total genetic differentiation among the different breeds. The genetic differentiation (pairwise FST ) among the eight Indian breeds varied from 0.0126 for the Kankrej-Malvi pair to 0.2667 for Khillar-Kenkatha pair. The phylogeny, principal components analysis, and structure analysis further supported close grouping of Kankrej, Malvi, Nimari and Gir; Gaolao and Kenkatha, whereas Dangi and Khillar remained at distance from other breeds. PMID:23216283

Shah, Tejas M; Patel, Jaina S; Bhong, Chandrakant D; Doiphode, Aakash; Umrikar, Uday D; Parmar, Shivnandan S; Rank, Dharamshibhai N; Solanki, Jitendra V; Joshi, Chaitanya G

2012-12-06

188

Maintenance of genetic diversity through plant-herbivore interactions.  

PubMed

Identifying the factors governing the maintenance of genetic variation is a central challenge in evolutionary biology. New genomic data, methods and conceptual advances provide increasing evidence that balancing selection, mediated by antagonistic species interactions, maintains genome-wide functionally important genetic variation within species and natural populations. Because diverse interactions between plants and herbivorous insects dominate terrestrial communities, they provide excellent systems to address this hypothesis. Population genomic studies of Arabidopsis thaliana and its relatives suggest spatial variation in herbivory maintains adaptive genetic variation controlling defense phenotypes, both within and among populations. Conversely, inter-species variation in plant defenses promotes adaptive genetic variation in herbivores. Emerging genomic model herbivores of Arabidopsis could illuminate how genetic variation in herbivores and plants interact simultaneously. PMID:23834766

Gloss, Andrew D; Nelson Dittrich, Anna C; Goldman-Huertas, Benjamin; Whiteman, Noah K

2013-07-05

189

Inferring recent historic abundance from current genetic diversity.  

PubMed

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

Palsbøll, Per J; Zachariah Peery, M; Olsen, Morten T; Beissinger, Steven R; Bérubé, Martine

2012-11-26

190

Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidis  

PubMed Central

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

Miragaia, Maria; de Lencastre, Herminia; Perdreau-Remington, Francoise; Chambers, Henry F.; Higashi, Julie; Sullam, Paul M.; Lin, Jessica; Wong, Kester I.; King, Katherine A.; Otto, Michael; Sensabaugh, George F.; Diep, Binh An

2009-01-01

191

Synthetic biology: advancing the design of diverse genetic systems.  

PubMed

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

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

2013-02-13

192

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.

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

2013-01-01

193

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

PubMed Central

Studies of structure-function relationships in the respiratory proteins of marine mammals revealed unexpected variations in the number and types of hemoglobins (Hbs) present in coastal bottlenose dolphins, Tursiops truncatus. We obtained blood samples from free-ranging coastal bottlenose dolphins as a component of capture-release studies. We found that the oxygen-binding functions of bottlenose dolphin blood are poised between effector-saturated and unsaturated levels, enabling exercise-dependent shifts in oxygen transfer functions. Isolated bottlenose dolphin Hbs showed elevated pH sensitivities (Bohr effects) and appreciably lower oxygen affinities than adult human Hb in the absence of allosteric effectors. These properties may be an adaptive modification that enhance oxygen delivery during diving episodes when oxygen tensions and effector levels are low. The Hbs of individual dolphins showed similar oxygen affinities, responses to effectors, and expression of heme-heme interaction in oxygen binding, but differed in their redox potentials and rates of autoxidation. The heterogeneity suggested by these functional variations in Hbs of individual dolphins was born out by variations in the molecular weights and numbers of their ? and ? globin chains. Although coastal bottlenose dolphins were expected to have a single type of Hb, the mass differences observed revealed considerable genetic diversity. There were multiple Hb forms in some individuals and differences in Hb patterns among individuals within the same community.

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

2007-01-01

194

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.

Bell, J.J; Okamura, B

2005-01-01

195

Molecular genetic diversity of Satureja bachtiarica.  

PubMed

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

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

2013-10-06

196

Defining the landscape of adaptive genetic diversity.  

PubMed

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.). PMID:22676074

Eckert, Andrew J; Dyer, Rodney J

2012-06-01

197

Genetic diversity and population genetic structure of saltmarsh Spartina alterniflora from four coastal Louisiana basins  

Microsoft Academic Search

Seventy-two Spartina alterniflora accessions originating from four coastal Louisiana basins (18 accessions per basin) were used to evaluate the genetic structure of this native perennial low-intertidal plant species. The objective of this study was to determine the population genetic structure and diversity of S. alterniflora accessions originating from these four basins using amplified fragment length polymorphism (AFLP) markers. A total

Herry S. Utomo; Ida Wenefrida; Michael D. Materne; Stephen A. Harrison

2009-01-01

198

Genetic diversity and multilocus genetic structure in the relictual endemic herb Japonolirion osense (Petrosaviaceae)  

Microsoft Academic Search

Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic

Akihiko Hoya; Hideki Takahashi; Masashi Ohara

2004-01-01

199

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

PubMed Central

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

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

2011-01-01

200

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

201

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

202

Population connectivity buffers genetic diversity loss in a seabird  

PubMed Central

Background Ancient DNA has revolutionized conservation genetic studies as it allows monitoring of the genetic variability of species through time and predicting the impact of ecosystems’ threats on future population dynamics and viability. Meanwhile, the consequences of anthropogenic activities and climate change to island faunas, particularly seabirds, remain largely unknown. In this study, we examined temporal changes in the genetic diversity of a threatened seabird, the Cory’s shearwater (Calonectris borealis). Findings We analysed the mitochondrial DNA control region of ancient bone samples from the late-Holocene retrieved from the Canary archipelago (NE Atlantic) together with modern DNA sequences representative of the entire breeding range of the species. Our results show high levels of ancient genetic diversity in the Canaries comparable to that of the extant population. The temporal haplotype network further revealed rare but recurrent long-distance dispersal between ocean basins. The Bayesian demographic analyses reveal both regional and local population size expansion events, and this is in spite of the demographic decline experienced by the species over the last millennia. Conclusions Our findings suggest that population connectivity of the species has acted as a buffer of genetic losses and illustrate the use of ancient DNA to uncover such cryptic genetic events.

2013-01-01

203

Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp.  

PubMed

The genetic diversity of 45 bradyrhizobial isolates that nodulate several Lupinus and Ornithopus species in different geographic locations was investigated by 16S rDNA PCR-RFLP and sequence analysis, 16S-23S rDNA intergenic spacer (IGS) PCR-RFLP analysis, and ERIC-PCR genomic fingerprinting. Reference strains of Bradyrhizobium japonicum, B. liaoningense and B. elkanii and some Canarian isolates from endemic woody legumes in the tribe Genisteae were also included. The 16S rDNA-RFLP analysis resolved 9 genotypes of lupin isolates, a group of fourteen isolates presented restriction-genotypes identical or very similar to B. japonicum, while another two main groups of isolates (69%) presented genotypes that clearly separated them from the reference species of soybean. 16S rDNA sequencing of representative strains largely agreed with restriction analysis, except for a group of six isolates, and showed that all the lupin isolates are relatives of B. japonicum, but different lineages were observed. The 16S-23S IGS-RFLP analysis showed a high resolution level, resolving 19 distinct genotypes among 30 strains analysed, and so demonstrating the heterogeneity of the 16S-RFLP groups. ERIC-PCR fingerprint analysis showed an enormous genetic diversity producing a different pattern for each but two of the isolates. Phylogeny of nodC gene was independent from the 16S rRNA phylogeny, and showed a tight relationship in the symbiotic region of the lupin isolates with isolates from Canarian genistoid woody legumes, and in concordance, cross-nodulation was found. We conclude that Lupinus is a promiscuous host legume that is nodulated by rhizobia with very different chromosomal genotypes, which could even belong to several species of Bradyrhizobium. No correlation among genomic background, original host plant and geographic location was found, so, different chromosomal genotypes could be detected at a single site and in a same plant species, on the contrary, an identical genotype was detected in very different geographical locations and plants. PMID:14666990

Jarabo-Lorenzo, Adriana; Pérez-Galdona, Ricardo; Donate-Correa, Javier; Rivas, Raúl; Velázquez, Encarna; Hernández, Mariano; Temprano, Francisco; Martínez-Molina, Eustoquio; Ruiz-Argüeso, Tomás; León-Barrios, Milagros

2003-11-01

204

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.

Liu, F; Zhang, L; Charlesworth, D

1998-01-01

205

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

PubMed Central

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

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

2010-01-01

206

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.

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

2010-01-01

207

Gene flow and genetic diversity of a broadcast-spawning coral in northern peripheral populations.  

PubMed

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 (F(ST) < or = 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

2010-06-16

208

Plant genetic diversity in the Canary Islands: a conservation perspective.  

PubMed

The Canary Islands are an Atlantic volcanic archipelago with a rich flora of ?570 endemic species. The endemics represent ?40% of the native flora of the islands, and ?20% of the endemics are in the E (endangered) category of the International Union for Conservation of Nature. A review of allozyme variation in 69 endemic species belonging to 18 genera and eight families is presented. The average species-level genetic diversity (H(T)) at allozyme loci is 0.186, which is twice as high as the mean reported for endemics of Pacific archipelagos. Possible factors contributing to this higher diversity are discussed, but the reasons remain obscure. An average of 28% of the allozyme diversity within species resides among populations, indicating a high level of interpopulational differentiation. Studies of reproductive biology indicate that many of the endemic species are outcrossers. The high total diversity within species, the relatively high differentiation among populations, and the outcrossing breeding systems have implications for species conservation. Decreased population sizes in outcrossing species would promote biparental inbreeding and increase inbreeding depression. The relatively high proportion of allozyme diversity among populations indicates that the most effective strategy for preserving genetic variation in species is to conserve as many populations as possible. The genetic diversity in many Canary Island endemics is endangered by: (1) overgrazing by introduced animals, such as barbary sheep, goats, mouflons, rabbits, and sheep; (2) interspecific hybridization following habitat disturbance or planting of endemics along roadsides or in public gardens; (3) competition with alien plant species; and (4) decline of population size because of urban development and farming. PMID:10898768

Francisco-Ortega, J; Santos-Guerra, A; Kim, S C; Crawford, D J

2000-07-01

209

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

PubMed

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

2013-08-07

210

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.

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

2013-01-01

211

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.

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

2011-01-01

212

Genetic diversity of the narrow endemic Astragalus oniciformis (Fabaceae).  

PubMed

Astragalus oniciformis Barneby is a narrow endemic xerophyte of the upper Snake River Plain of central Idaho, USA, where it inhabits stabilized, aeolian sand deposits and previously burned, sandy sites over Quaternary basalt flows. The objective of this study was to determine the levels and distribution of genetic differentiation within and among populations of A. oniciformis. Fifteen individuals from each of eight populations, chosen from throughout the range of the species, were selected based on accessibility, density of individuals, and large population size. Inter-simple sequence repeats were chosen as the marker to assess genetic differentiation. The two primers selected yielded 40 polymorphic loci in A. oniciformis. In an analysis of molecular variance, 88.69% of the variation was significantly attributed to variation within populations. High gene flow (N(m) = 3.91-3.93; SD = 0.01) and a low percentage deviation from Hardy-Weinberg equilibrium due to population subdivision (G(ST) = 0.113-0.1134; SD = 0.0002) were found among sampled populations. These results suggest that current threats to this species, including changing fire patterns and habitat loss from grazing disturbance, have not yet affected the genetic diversity of this species. Preservation of large populations and smaller, intervening, dispersed patches will help preserve the genetic integrity and the genetic diversity found in A. oniciformis. PMID:21652349

Alexander, J Andrew; Liston, Aaron; Popovich, Steve J

2004-12-01

213

Glacial refugia: hotspots but not melting pots of genetic diversity.  

PubMed

Glacial refuge areas are expected to harbor a large fraction of the intraspecific biodiversity of the temperate biota. To test this hypothesis, we studied chloroplast DNA variation in 22 widespread European trees and shrubs sampled in the same forests. Most species had genetically divergent populations in Mediterranean regions, especially those with low seed dispersal abilities. However, the genetically most diverse populations were not located in the south but at intermediate latitudes, a likely consequence of the admixture of divergent lineages colonizing the continent from separate refugia. PMID:12791991

Petit, Rémy J; Aguinagalde, Itziar; de Beaulieu, Jacques-Louis; Bittkau, Christiane; Brewer, Simon; Cheddadi, Rachid; Ennos, Richard; Fineschi, Silvia; Grivet, Delphine; Lascoux, Martin; Mohanty, Aparajita; Müller-Starck, Gerhard; Demesure-Musch, Brigitte; Palmé, Anna; Martín, Juan Pedro; Rendell, Sarah; Vendramin, Giovanni G

2003-06-01

214

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.

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

215

Genetic diversity among geographically separated populations of Nepenthes mirabilis  

Microsoft Academic Search

The distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central\\u000a (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations\\u000a were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals\\u000a produced 75.18%

Arunrat Chaveerach; Alongkod Tanomtong; Runglawan Sudmoon; Tawatchai Tanee

2006-01-01

216

Genetic diversity among native isolates of rhizobia from Phaseolus lunatus  

Microsoft Academic Search

The genetic diversity among native nodular rhizobia of Lima bean in soil from Piauí State, Brazil, was characterized and evaluated.\\u000a The genotype UFPI-491 was used as a trap plant for rhizobia, with soil samples collected in Piaui State being used as the\\u000a inoculum source. For isolation, nodules were collected at 45 days after seedling emergence—a period that presented the highest\\u000a values

Jardel Oliveira Santos; Jadson Emanuel Lopes Antunes; Ademir Sergio Ferreira Araújo; Maria Carmo Catanho Pereira Lyra; Regina Lúcia Ferreira Gomes; Angela Celis Almeida Lopes; Márcia Vale Barreto Figueiredo

217

Genetic composition of Jewish populations: diversity and inbreeding.  

PubMed

Genetic diversity and F statistics analysis, using 9 and 5 blood group loci, respectively, were carried out on 16 Jewish populations from 5 geographic regions: East Europe, Central Europe, South Europe, Middle East and North Africa. The proportion of total diversity found within populations was 98.9% while that between populations, within geographic groups and between groups altogether was only 1.1%. The average heterozygosity between geographic groups ranged from 0.3867 to 0.4150. There were no significant differences between geographic groups of populations in heterozygosity or in its variance. Average estimates of inbreeding were as follows: Fis = 0.0419, Fst = 0.0084 and Fit = 0.0498. Because the heterogeneity and relative proportion of diversity were less between Jewish populations than between non-Jewish ones, we conclude that genetic similarity between Jews is higher than between Gentiles. The findings are in agreement with our previously obtained calculations of genetic distances (Kobyliansky, Micle, Goldschmidt-Nathan, Arensburg and Nathan 1982). PMID:6638941

Kobyliansky, E; Livshits, G

218

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.

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

2012-01-01

219

An Investigation of Relationships among Genetic Counselors’ Supervision Skills and Multicultural Counseling Competence  

Microsoft Academic Search

As racial and ethnic diversity increase in the U.S., genetic counselor multicultural competence is growing in importance.\\u000a In mental health counseling, supervisor multicultural competence has been shown to promote supervisees’ multicultural competence.\\u000a Moreover, developmentally-advanced supervisors tend to be more effective. This study was designed to investigate relationships\\u000a among genetic counselor supervisors’ perceived multicultural counseling competence and development as supervisors, and

Hyun Kyung Lee; Patricia McCarthy Veach; Bonnie S. LeRoy

2009-01-01

220

Functional roles affect diversity-succession relationships for boreal beetles.  

PubMed

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

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

2013-08-20

221

[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

222

The Willamette Valley Seed Increase Program: developing genetically diverse germplasm using an ecoregion approach  

Microsoft Academic Search

The goal of the Institute for Applied Ecology’s Willamette Valley Seed Increase Program is to develop a supply of ecologically appropriate, genetically diverse native plant material for restoration of prairie ecosystems in the Willamette Valley. In creating restoration germplasm we seek to maximize genetic diversity while simultaneously protecting genetic integrity of extant native populations. In the absence of genetic data

Kimiora Ward; Melanie Gisler; Rob Fiegener; Amy Young

2008-01-01

223

Assessing the contribution of breeds to genetic diversity in conservation schemes  

Microsoft Academic Search

The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the

Herwin Eding; Richard PMA Crooijmans; Martien AM Groenen; Theo HE Meuwissen

2002-01-01

224

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

PubMed

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

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

2013-08-01

225

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice ( Oryza rufipogon Griff.) in China  

Microsoft Academic Search

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18

Hai-fei Zhou; Zhong-wen Xie; Song Ge

2003-01-01

226

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.

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

2011-01-01

227

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

Microsoft Academic Search

Summary 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

YASUKO YOSHIDA; MASANORI HONJO; NAOKO KITAMOTO; RYO OHSAWA

2009-01-01

228

Selecting subsets of genotyped experimental populations for phenotyping to maximize genetic diversity.  

PubMed

Selective phenotyping is a way of capturing the benefits of large population sizes without the need to carry out large-scale phenotyping and hence is a cost-effective means of capturing information about gene-trait relationships within a population. The diversity within the sample gives an indication of the efficiency of this information capture; less diversity implies greater redundancy of the genetic information. Here, we propose a method to maximize genetic diversity within the selected samples. Our method is applicable to general experimental designs and robust to common problems such as missing data and dominant markers. In particular, we discuss its application to multi-parent advanced generation intercross (MAGIC) populations, where, although thousands of lines may be genotyped as a large population resource, only hundreds may need to be phenotyped for individual studies. Through simulation, we compare our method to simple random sampling and the minimum moment aberration method. While the gain in power over simple random sampling for all tested methods is not large, our method results in a much more diverse sample of genotypes. This diversity can be applied to improve fine mapping resolution once a QTL region has been detected. Further, when applied to two wheat datasets from doubled haploid and MAGIC progeny, our method detects known QTL for small sample sizes where other methods fail. PMID:23052022

Emma Huang, B; Clifford, David; Cavanagh, Colin

2012-10-05

229

[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

230

Assessment of genetic diversity within and between pearl millet landraces.  

PubMed

A minimum core subset of pearl millet [ Pennisetum glaucum (L.) R. Br.], which comprised 504 landrace accessions, was recently established from the global pearl millet germplasm collection of ICRISAT. The accessions for this core were selected by a random proportional sampling strategy following stratification of the entire landrace collection (about 16,000 accessions) according to their geographic origin and morpho-agronomic traits. In this study RFLP probes were used to quantify the genetic diversity within and between landrace accessions of this minimum core using a subset comprising ten accessions of Indian origin. Twenty five plants per accession were assayed with EcoRI, EcoRV, HindIII and DraI restriction enzymes, and 16 highly polymorphic RFLP probes, nine associated with a quantitative trait loci (QTLs) for downy mildew resistance, and five associated with a QTL for drought tolerance. A total of 51 alleles were detected using 16 different probe-enzyme combinations. The partitioning of variance components based on the analysis of molecular variance (AMOVA) for diversity analysis revealed high within-accession variability (30.9%), but the variability between accessions was significantly higher (69.1%) than that within the accessions. A dendrogram based on the dissimilarity matrix obtained using Ward's algorithm further delineated the 250 plants into ten major clusters, each comprised of plants from a single accession (with the exception of two single plants). A similar result was found in an earlier study using morpho-agronomic traits and geographic origin. This study demonstrated the utility of RFLP markers in detecting polymorphism and estimating genetic diversity in a highly cross-pollinated species such as pearl millet. When less-tedious marker systems are available, this method could be further extended to assess the genetic diversity between and within the remaining accessions in the pearl millet core subset. PMID:12582479

Bhattacharjee, Ranjana; Bramel, J.; Hash, T.; Kolesnikova-Allen, A.; Khairwal, S.

2002-08-01

231

Diachronic (1979–2003) analysis of rice genetic diversity in Guinea did not reveal genetic erosion  

Microsoft Academic Search

Greater insight into the dynamics of genetic resources of crop plants is needed in order to pinpoint detrimental evolutionary\\u000a patterns and draw up conservation priorities. Temporal evolution of rice genetic diversity was monitored in Maritime Guinea\\u000a where subsistence-oriented agriculture prevails. Diachronic comparison was performed between samples collected in six villages\\u000a during the 1979\\/1982-period and in 2003, based on the names

Mamdou B. Barry; Jean Louis Pham; Sedou Béavogui; Alain Ghesquière; Nour Ahmadi

2008-01-01

232

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.

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

2011-01-01

233

In Situ conservation of maize in Mexico: Genetic diversity and Maize seed management in a traditional community  

Microsoft Academic Search

Results from a study of maize varieties and seed sources in a traditional community in Jalisco, Mexico, raise questions about\\u000a the relationship between genetic erosion and the introduction of varieties. The relevance of models for in situ conservation\\u000a of crop genetic resources based on geographical isolation of a community is discussed. The morphophenological diversity of\\u000a local materials is shown to

Dominique Louette; André Charrier; Julien Berthaud

1997-01-01

234

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

2012-08-16

235

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.

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

2013-01-01

236

Genetic diversity and molecular evolution of chinese waxy maize germplasm.  

PubMed

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

2013-06-20

237

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

2012-04-18

238

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.

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

2012-01-01

239

Habitat islands, genetic diversity, and gene flow in a Patagonian rodent.  

PubMed

The effects of terrestrial habitat islands on gene flow and genetic diversity in animal populations have been predicted and discussed in theoretical terms, but empirical data are needed to test these predictions and provide an understanding of the relationships of life-history characteristics to genetics of insular species. We studied saxicolous mice (Phyllotis xanthopygus) in Patagonia to explore genetic structure, phylogeography, and gene flow in a species inhabiting natural habitat islands. Phylogeographic analyses based on mtDNA sequences revealed two haplotype clades, which presumably reflect early Pleistocene factors that temporarily separated the mice into two geographically isolated groups. The Río Chubut, which lies within a glacial drainage basin bisecting northern Patagonia, might have affected gene flow in the species. Although we anticipated isolation by distance and founder phenomena associated with habitat islands, in some habitat patches we found evidence of high local genetic diversity. The amount of divergence in the mitochondrial cytochrome b gene (approximately 3.4%) in animals at a single locality could best be explained through a combination of historical factors and metapopulation source-sink theory. Demographic shifts, dispersal, and episodic recolonization are important in the life history and genetic population structure of P. xanthopygus. PMID:9640647

Kim, I; Phillips, C J; Monjeau, J A; Birney, E C; Noack, K; Pumo, D E; Sikes, R S; Dole, J A

1998-06-01

240

Molecular analysis for genetic diversity and distance of introduced Grus antigone sharpii L. to Thailand.  

PubMed

The genetic relationship was examined in a population of Grus antigone sharpii L. using DNA markers from the ISSR technique for applying towards breeding purposes for conservation of species. Since their extinction from Thailand, sixteen eastern sarus cranes: Grus antigone sharpii L. provided from Cambodia were fed and bred to sixty individuals at Nakhonratchasima Zoo, Northeastern Thailand to re-exist in Thai natural sites. Their genetic diversity and distance were examined to test their possibility to adapt to environmental variation. Blood samples from 27 individuals of Grus antigone sharpii L. were collected and DNA was extracted. These DNA samples were amplified using the successful fifteen from twenty four primers inter simple sequences repeat markers. A dendrogram was constructed and shows distance values of the species between 12.1 and 53.5. The samples produced 63.96% polymorphic banding profiles. The genetic diversity (H') in this population was estimated using Shannon's index. The high H' value of 0.501 reflected the somewhat wide range of distribution sites, which would adapt to environmental variations. Genetic evenness is 0.152. This value supports that all the studied samples have a small equal genetic abundance. PMID:19579938

Tanee, T; Chaveerach, A; Anuniwat, A; Tanomtong, A; Pinthong, K; Sudmoon, R; Mokkamul, P

2009-01-15

241

Polymorphic Alu insertions and genetic diversity among African populations.  

PubMed

Thorough assessment of modern genetic diversity and interpopulation affinities within the African continent is essential for understanding the processes that have been at work during the course of worldwide human evolution. Regardless of whether autosomal, Y-chromosome, or mtDNA markers are used, allele- or haplotype-frequency data from African populations are necessary in setting the framework for the construction of global population phylogenies. In the present study we analyze genetic differentiation and population structure in a data set of nine African populations using 12 polymorphic Alu insertions (PAls). Furthermore, to place our findings within a global context, we also examined an equal number of non-African groups. Frequency data from 456 individuals presented for the first time in this work plus additional data obtained from the literature indicate an overall pattern of higher intrapopulation diversity in sub-Saharan populations than in northern Africa, a prominent differentiation between these two locations, an appreciably high degree of transcontinental admixture in Egypt, and significant discontinuity between Morocco and the Iberian peninsula. Moreover, the topologies of our phylogenetic analyses suggest that out of the studied sub-Saharan groups, the southern Bantu population of Sotho/ Tswana presents the highest level of antiquity, perhaps as a result of ancestral or acquired Khoisan genetic signals. Close affinities of eastern sub-Saharan populations with Egypt in the phylogenetic trees may indicate the existence of gene flow along the Nile River. PMID:16596946

Terreros, Maria C; Martinez, Laisel; Herrera, Rene J

2005-10-01

242

Genetic variation in biomass traits among 20 diverse rice varieties.  

PubMed

Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops. PMID:21062890

Jahn, Courtney E; Mckay, John K; Mauleon, Ramil; Stephens, Janice; McNally, Kenneth L; Bush, Daniel R; Leung, Hei; Leach, Jan E

2010-11-09

243

Functional consequences of genetic diversity in Strongyloides ratti infections.  

PubMed Central

Parasitic nematodes show levels of genetic diversity comparable to other taxa, but the functional consequences of this are not understood. Thus, a large body of theoretical work highlights the potential consequences of parasite genetic diversity for the epidemiology of parasite infections and its possible implications for the evolution of host and parasite populations. However, few relevant empirical data are available from parasites in general and none from parasitic nematodes in particular. Here, we test two hypotheses. First, that different parasitic nematode genotypes vary in life-history traits, such as survivorship and fecundity, which may cause variation in infection dynamics. Second, that different parasitic nematode genotypes interact within the host (either directly or via the host immune system) to increase the mean reproductive output of mixed-genotype infections compared with single-genotype infections. We test these hypotheses in laboratory infections using genetically homogeneous lines of Strongyloides ratti. We find that nematode genotypes do vary in their survivorship and fecundity and, consequently, in their dynamics of infection. However, we find little evidence of interactions between genotypes within hosts under a variety of trickle- and single-infected infection regimes.

Paterson, S; Viney, M E

2003-01-01

244

Allozyme Evidence for Genetic Autopolyploidy and High Genetic Diversity in Tetraploid Cranberry, Vaccinium oxycoccos (Ericaceae)  

Microsoft Academic Search

Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation.

Gregory Mahy; Leo P. Bruederle; Bridget Connors; Michael Van Hofwegen; Nicholi Vorsa

2000-01-01

245

Analysis of molecular genetic diversity of cardoon (Cynara cardunculus L.) in Tunisia.  

PubMed

The objective of this study is to investigate the genetic diversity, the relationships among six Tunisian wild cardoon populations (Cynara cardunculus var. sylvestris) and a Tunisian's population of cultivated cardoon (Cynara cardunculus var. altilis DC) in seven different geographical locations (Tiurif, Bahra, Zriba, Bouficha, Enfidha, Beja and Wad mliz) from semi-arid and wet regions of Tunisia. Twenty-three selected microsatellite markers are used for a sample of 98 cardoon genotypes. The total of 243 alleles is detected in the studied populations and the number of alleles per locus ranged from six to 23. The dendrogram based on Nei's (1972) UPGMA method divides the seven studied populations to five clusters. These preliminary results show that microsatellites are effective tools for plant species characterization and the analysed populations have a high genetic variability and will be suitable as genetic stocks for conservation and sustainable utilization programs of Cynara cardunculus L. in Tunisia. PMID:22721560

Khaldi, Soumaya; Sonnante, Gabriella; El Gazzah, Mohammed

2012-05-25

246

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.

Spurgin, Lewis G.; Richardson, David S.

2010-01-01

247

Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci.  

PubMed

Conservation and improvement strategies in farm animals should be based on a combination of genetic and phenotypic characteristics. Genotype data from 30 microsatellites were used to assess the genetic diversity and relationships among five Cuban cattle breeds (Siboney de Cuba, Criollo Cubano, Cebú Cubano, Mambí de Cuba and Taíno de Cuba). All microsatellite markers were highly polymorphic in all the breeds. The expected heterozygosity ranged from 0.67 ± 0.02 in the Taíno de Cuba breed to 0.75 ± 0.02 in the Mambí de Cuba breed, and the observed heterozygosity ranged from 0.66 ± 0.03 in the Cebú Cubano breed to 0.73 ± 0.02 in the Siboney de Cuba breed. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F(ST)). The exact test for Hardy-Weinberg equilibrium within breeds showed a significant deviation in each breed (p < 0.0003) for one or more loci. The genetic distance and structure analysis showed that a significant amount of genetic variation is maintained in the local cattle population and that all breeds studied could be considered genetically distinct. The Siboney de Cuba and Mambí de Cuba breeds seem to be the most genetically related among the studied five breeds. PMID:23317068

Acosta, A C; Uffo, O; Sanz, A; Ronda, R; Osta, R; Rodellar, C; Martin-Burriel, I; Zaragoza, P

2012-02-09

248

Genetic diversity of the natural populations of Arabidopsis thaliana in China.  

PubMed

Although extensive studies have been conducted on the genetic structure of Arabidopsis thaliana (A. thaliana) populations worldwide, the populations from China have never been studied. In this study, we collected 560 individuals from 19 natural populations of A. thaliana distributed in East China along the lower reaches of the Yangtze River, and two populations from northwest China (Xinjiang Province). We adopted two kinds of molecular marker, inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPDs) to investigate the genetic diversity within and among populations, and the correlation between the genetic and geographic distances. Thirteen ISSR primers produced 165 polymorphic bands (PPB) (96%) and 11 RAPD primers produced 162 polymorphic bands (98%) in about 560 individuals. The two marker systems generated similar patterns of genetic diversity in these natural populations. The AMOVA analysis indicated about 42-45% of the total genetic variation existed within populations, and found possible geographic structure. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. A close genetic relationship was found among four populations in the Jiangxi Province, and these always appeared clustered together as a monophyletic group in unweighted pair-group method with arithmetic averages dendrograms based on both ISSR and RAPD data sets. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity. PMID:17593944

He, F; Kang, D; Ren, Y; Qu, L-J; Zhen, Y; Gu, H

2007-06-27

249

Phylogenetic relationships and diversity of ?-rhizobia associated with Mimosa species grown in Sishuangbanna, China.  

PubMed

In order to investigate the genetic diversity of rhizobia associated with various exotic and invasive species in tropical mainland China, 116 bacterial isolates were obtained from Mimosa root nodules collected from Sishuangbanna and Yuanjiang districts of Yunnan province. Isolated rhizobia were characterized by RFLP analysis of 16S rRNA genes, SDS-PAGE of whole-cell proteins and BOX-PCR. Most of the isolated strains were identified as ?-rhizobia belonging to diverse populations of Burkholderia and Cupriavidus, and the phylogenetic relationships of their 16S rRNA gene sequences showed that they were closely related to one of four ?-rhizobia species: Burkholderia phymatum, B. mimosarum, B. caribensis or Cupriavidus taiwanensis. Additionally, among the 116 isolates, 53 different whole-cell SDS-PAGE profiles and 30 distinct BOX-PCR genotypic patterns were detected, which demonstrated the genetic and phenotypic diversity found within these Burkholderia and Cupriavidus strains. To the best of our knowledge, this is the first report that ?-rhizobia are extant and possibly widespread on the Chinese mainland and nodulate easily with Mimosa plants. We also find it especially interesting that this appears to be the first report from mainland China of Cupriavidus symbionts of Mimosa. These records enrich our knowledge and understanding of the geographical distribution and diversity of these bacteria. PMID:20228206

Liu, Xiao Yun; Wu, Wei; Wang, En Tao; Zhang, Bin; Macdermott, Jomo; Chen, Wen Xin

2010-03-12

250

Genetic Diversity of Neisseria lactamica Strains from Epidemiologically Defined Carriers  

PubMed Central

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

Alber, Dirk; Oberkotter, Mark; Suerbaum, Sebastian; Claus, Heike; Frosch, Matthias; Vogel, Ulrich

2001-01-01

251

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.

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

2011-01-01

252

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

253

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes  

Microsoft Academic Search

Plant genetic resources are important sources of genetic variation for improving crop varieties as breeding materials. Conservation\\u000a of such resources of allogamous species requires maintenance of the genetic diversity within each accession to avoid inbreeding\\u000a depression and loss of rare alleles. For assessment of genetic diversity in the self-incompatibility locus (S locus), which is critically involved in the chance of

S. Takuno; E. Oikawa; H. Kitashiba; T. Nishio

2010-01-01

254

The Genomic Diversity and Phylogenetic Relationship in the Family Iridoviridae  

PubMed Central

The Iridoviridae family are large viruses (?120–200 nm) that contain a linear double-stranded DNA genome. The genomic size of Iridoviridae family members range from 105,903 bases encoding 97 open reading frames (ORFs) for frog virus 3 to 212,482 bases encoding 211 ORFs for Chilo iridescent virus. The family Iridoviridae is currently subdivided into five genera: Chloriridovirus, Iridovirus, Lymphocystivirus, Megalocytivirus, and Ranavirus. Iridoviruses have been found to infect invertebrates and poikilothermic vertebrates, including amphibians, reptiles, and fish. With such a diverse array of hosts, there is great diversity in gene content between different genera. To understand the origin of iridoviruses, we explored the phylogenetic relationship between individual iridoviruses and defined the core-set of genes shared by all members of the family. In order to further explore the evolutionary relationship between the Iridoviridae family repetitive sequences were identified and compared. Each genome was found to contain a set of unique repetitive sequences that could be used in future virus identification. Repeats common to more than one virus were also identified and changes in copy number between these repeats may provide a simple method to differentiate between very closely related virus strains. The results of this paper will be useful in identifying new iridoviruses and determining their relationship to other members of the family.

Eaton, Heather E.; Ring, Brooke A.; Brunetti, Craig R.

2010-01-01

255

Genetic diversity and ecosystem functioning in the face of multiple stressors.  

PubMed

Species diversity is important for a range of ecosystem processes and properties, including the resistance to single and multiple stressors. It has been suggested that genetic diversity may play a similar role, but empirical evidence is still relatively scarce. Here, we report the results of a microcosm experiment where four strains of the marine diatom Skeletonema marinoi were grown in monoculture and in mixture under a factorial combination of temperature and salinity stress. The strains differed in their susceptibility to the two stressors and no strain was able to survive both stressors simultaneously. Strong competition between the genotypes resulted in the dominance of one strain under both control and salinity stress conditions. The overall productivity of the mixture, however, was not related to the dominance of this strain, but was instead dependent on the treatment; under control conditions we observed a positive effect of genetic richness, whereas a negative effect was observed in the stress treatments. This suggests that interactions among the strains can be both positive and negative, depending on the abiotic environment. Our results provide additional evidence that the biodiversity-ecosystem functioning relationship is also relevant at the level of genetic diversity. PMID:23028735

Roger, Fabian; Godhe, Anna; Gamfeldt, Lars

2012-09-18

256

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

PubMed

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

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

2013-02-27

257

GENETIC STRUCTURE AND DIVERSITY AMONG MAIZE INBRED LINES AS INFERRED FROM DNA MICROSATELLITES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Although the tremendous diversity of the maize genome has been well documented, the limited scope of previous studies failed to fully characterize the genetic structure and diversity inherent in the germplasm. In this study, 260 maize inbred lines, representing the majority of genetic diversity ava...

258

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

2013-03-23

259

Quantitative Evaluation of Genetic Diversity in Wheat Germplasm Using Molecular Markers  

Microsoft Academic Search

techniques used to characterize wheat cultivars (Vac- cino et al., 1993) and assess genetic diversity (Kim and Characterization of germplasm by means of DNA fingerprinting a quantitative estimate of genetic diversity. This estimate is important because a decrease in genetic variability might result in a reduction cultivars (Bryan et al., 1999) and the complexity and of the plasticity of the

M. M. Manifesto; A. R. Schlatter; H. E. Hopp; E. Y. Suárez; J. Dubcovsky

2001-01-01

260

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

261

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.

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

2013-01-01

262

Genetic Diversity within Cryptosporidium parvum and Related Cryptosporidium Species  

PubMed Central

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

Xiao, Lihua; Morgan, Una M.; Limor, Josef; Escalante, Ananias; Arrowood, Michael; Shulaw, William; Thompson, R. C. A.; Fayer, Ronald; Lal, Altaf A.

1999-01-01

263

Genetic diversity among toxigenic and nontoxigenic Vibrio cholerae O1 isolated from the Western Hemisphere.  

PubMed Central

Multilocus enzyme electrophoresis was used to examine genetic relationships among and between toxigenic and non-toxigenic isolates of Vibrio cholerae O1 obtained from patients and the environment in the US Gulf Coast and surrounding areas. A total of 23 toxigenic and 23 non-toxigenic strains were examined. All the toxigenic and 7 of the non-toxigenic strains had the same alleles at 16 enzyme loci, whereas the balance of the nontoxigenic strains had 9 distinct combinations of alleles. This study suggests that all of the toxigenic strains belong to a single clone, and that while some of the non-toxigenic isolates were related, most were of diverse origin.

Chen, F.; Evins, G. M.; Cook, W. L.; Almeida, R.; Hargrett-Bean, N.; Wachsmuth, K.

1991-01-01

264

Temporal change in the diversity-invasibility relationship in the presence of a disturbance regime.  

PubMed

Disturbance can affect both the diversity and invasibility of communities. Many field studies have found correlations between diversity and susceptibility to invasion, but if both factors independently respond to disturbance then spurious non-causal relationships may be observed. Here, we show that disturbance can cause a temporal shift in the diversity-invasibility relationship. In a field experiment using sessile marine communities, disturbance strongly affected both diversity and invasion such that they were highly correlated. Disturbance facilitated initial invasion, creating a negative diversity-invasibility relationship when the invader first arrived. Over time, disturbance hindered the persistence of invaders, creating a positive diversity-invasibility relationship. We suggest that temporal changes in the diversity-invasibility relationship may have contributed to the 'invasion paradox', a term for the contrasting patterns of experimental and observational studies of the diversity-invasibility relationship. PMID:21070561

Clark, Graeme F; Johnston, Emma L

2010-11-11

265

Genetic diversity of allozymes in turnip (Brassica rapa L. var. rapa) from the Nordic area.  

PubMed

Genetic diversity and relationships based on isozymes were studied in 31 accessions of turnip (Brassica rapa L. var. rapa). The material included varieties, elite stocks, landraces and older turnip of slash-and-burn type from the Nordic area. A total of 9 isozyme loci and 26 alleles were studied. The isozyme systems were ACO, DIA, GPI, GOT, PGM, PGD and SKD. The level of heterozygosity was reduced in the landraces, but it was high for the variety group 'Ostersundom'. Turnip has a higher genetic variation than other crops within B. rapa and than in other species with the same breeding system. The genetic diversity showed that 18.7% of the genetic variation was within the accessions, and the total H tau value was 0.358. Gpi-I and Pgd-I showed the lowest variation compared with the other loci. The cluster analysis revealed five clusters, with one main cluster including 25 of the 31 accessions. The dendrogram indicated that the variety group 'Ostersundom' clustered together whereas the variety group 'Bortfelder' was associated with country of origin. The landraces were spread in different clusters. The 'slash-and-burn' type of turnip belonged to two groups. PMID:11525064

Persson, K; Fält, A S; von Bothmer, R

2001-01-01

266

Genetics and Medicine: An Evolving Relationship  

ERIC Educational Resources Information Center

|Described is the importance of genetic factors in health and disease and calls for the development of services for genetic screening, diagnosis, and counseling. Such services presently available in Canada are described. (BB)|

Scriver, Charles R.; And Others

1978-01-01

267

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

PubMed

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

2011-05-11

268

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.

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

269

Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci.  

PubMed

The origin and relationships of Indian Muslims is still dubious and are not yet genetically well studied. In the light of historically attested movements into Indian subcontinent during the demic expansion of Islam, the present study aims to substantiate whether it had been accompanied by any gene flow or only a cultural transformation phenomenon. An array of 13 autosomal STR markers that are common in the worldwide data sets was used to explore the genetic diversity of Indian Muslims. The austere endogamy being practiced for several generations was confirmed by the genetic demarcation of each of the six Indian Muslim communities in the phylogenetic assessments for the markers examined. The analyses were further refined by comparison with geographically closest neighboring Hindu religious groups (including several caste and tribal populations) and the populations from Middle East, East Asia and Europe. We found that some of the Muslim populations displayed high level of regional genetic affinity rather than religious affinity. Interestingly, in Dawoodi Bohras (TN and GUJ) and Iranian Shia significant genetic contribution from West Asia, especially Iran (49, 47 and 46%, respectively) was observed. This divulges the existence of Middle Eastern genetic signatures in some of the contemporary Indian Muslim populations. Our study reveals that the spread of Islamic faith in the Indian subcontinent was predominantly cultural transformation associated with minor gene flow from West Asia. PMID:19424286

Eaaswarkhanth, Muthukrishnan; Dubey, Bhawna; Meganathan, Poorlin Ramakodi; Ravesh, Zeinab; Khan, Faizan Ahmed; Singh, Lalji; Thangaraj, Kumarasamy; Haque, Ikramul

2009-05-08

270

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

2012-08-08

271

Assessing ecosystem integrity of restored prairie wetlands from species production–diversity relationships  

Microsoft Academic Search

We assessed ecosystem integrity in restored prairie wetlands in eastern South Dakota, U.S.A., by examining the relationship between and diatom diversity and production. We asked three questions: (1) Is production related to species diversity? (2) Can production-diversity relationships be used to distinguish between restored and reference wetlands with the purpose of assessing ecological integrity? (3) Are production-diversity relationships influenced by

Paul M. Mayer; Susan M. Galatowitsch

2001-01-01

272

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

PubMed Central

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.

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

273

Role of telomere dysfunction in genetic intratumor diversity.  

PubMed

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

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

2011-01-01

274

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

PubMed

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, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

2013-03-04

275

Mutual feedbacks maintain both genetic and species diversity in a plant community.  

PubMed

The forces that maintain genetic diversity among individuals and diversity among species are usually studied separately. Nevertheless, diversity at one of these levels may depend on the diversity at the other. We have combined observations of natural populations, quantitative genetics, and field experiments to show that genetic variation in the concentration of an allelopathic secondary compound in Brassica nigra is necessary for the coexistence of B. nigra and its competitor species. In addition, the diversity of competing species was required for the maintenance of genetic variation in the trait within B. nigra. Thus, conservation of species diversity may also necessitate maintenance of the processes that sustain the genetic diversity of each individual species. PMID:17872447

Lankau, Richard A; Strauss, Sharon Y

2007-09-14

276

Genetic Diversity and Improvement of Contemporary Proprietary North American Dent Corn  

Microsoft Academic Search

Coeffi cient of parentage (CP) is useful to esti- mate genetic diversity (1 ? CP) among a set of lines. Estimated diversity among 846 proprietary inbred corn (Zea mays L.) lines registered in the United States from 1976 to 2005 shows favor- able diversity of 0.944. Less diversity (0.859) was found among 47 widely grown hybrids from 1995 to 2001.

Mark A. Mikel; Roy J. Carver

2008-01-01

277

SEQUENCE-BASED AMPLIFIED POLYMORPHISMS ARE USEFUL FOR STUDYING GENETIC DIVERSITY OF WINTER SQUASH  

Technology Transfer Automated Retrieval System (TEKTRAN)

Germplasm conservation facilities require an accurate understanding of the patterns of genetic diversity within and among accessions (unique populations) that comprise germplasm collections and the ecogeographical patterns of this diversity. This information facilitates the efficient management of g...

278

Genetic diversity of Plasmodium vivax isolates from Azerbaijan  

PubMed Central

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

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

2004-01-01

279

Genetic diversity of 'Ubá' mango tree using ISSR markers.  

PubMed

In this study, the genetic diversity of 'Ubá' mango trees cultivated at the Zona da Mata of Minas Gerais State, Brazil, was assessed, to identify whether there is variability in the plants grown in the region, justifying the mass selection as a breeding method. We used 102 accessions. Leaves were collected for extraction of genomic DNA, which was amplified with nine ISSR primers. The data obtained by the analysis of electrophoretic patterns were arranged in a binary matrix, considering 0 for the absence and 1 for the presence of bands. Based on these data, we performed the analysis of genetic dissimilarity and carried out the cluster analysis by the methods of Tocher and graphical dispersion. The most similar accessions are 144 and 150, both coming from Ubá, while the most divergent ones are 29 and 97, from Visconde do Rio Branco. The grouping by the Tocher method separated the accessions into six groups, 94.1% of which were allocated in the first group and showed that there is no separation of accessions depending on the sampling sites. The 3D scatter plot reinforces this conclusion. There is genetic variability among the accessions of 'Ubá' mango tree evaluated. Therefore, it is possible to make mass selection in open-pollinated populations. PMID:21644009

Rocha, Aline; Salomão, Luiz Carlos Chamhum; Salomão, Tânia Maria Fernandes; Cruz, Cosme Damião; de Siqueira, Dalmo Lopes

2012-02-01

280

Genetic diversity through the looking glass: Effect of enrichment bias  

SciTech Connect

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D{sup +}) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burk holderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfd4 and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D{sup +} populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques. 34 refs., 4 figs., 1 tab.

Dunbar, J.; Forney, L. [Michigan State Univ., East Lansing, MI (United States); White, S. [Los Alamos National Lab., NM (United States)

1997-04-01

281

Distribution of genetic diversity among disjunct populations of the rare forest understory herb, Trillium reliquum  

Microsoft Academic Search

We assessed genetic diversity and its distribution in the rare southeastern US forest understory species, Trillium reliquum. In all, 21 loci were polymorphic (PS=95.5%) and the mean number of alleles per polymorphic locus was 3.05. However, genetic diversity was relatively low (Hes=0.120) considering the level of polymorphism observed for this outcrossing species. A relatively high portion of the genetic diversity

E Gonzales; J L Hamrick

2005-01-01

282

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

PubMed

The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten microsatellie loci had high or medium polymorphism in these Amur tigers and had high genetic diversity. At the same time, we only found even bases variability which showed the even bases repeat sequence (CA/GT) maybe the basic unit for length variability of microsatellite in all loci. In this study, the samples were made up of 75 hair specimens, 23 blood specimens and 15 tissue specimens, we obtained the genome DNA from hairs using the non-invasive DNA technology and demonstrated that DNA derived from hair samples is as good as that obtained from blood samples for the analysis of microsatellite polymorphism. These results imply that microsatellite DNA markers and non-invasive DNA technology can help study the genetic diversity of Amur tiger. This method could be used in the captive management of other endangered species. PMID:15640074

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

2004-09-01

283

Genetic diversity in bambara groundnut (Vigna subterranea (L.) Verdc) landraces revealed by AFLP markers.  

PubMed

Bambara groundnut (Vigna subterranea (L.) Verdc), an African indigenous legume, is popular in most parts of Africa. The present study was undertaken to establish genetic relationships among 16 cultivated bambara groundnut landraces using fluorescence-based amplified fragment length polymorphism (AFLP) markers. Seven selective primer combinations generated 504 amplification products, ranging from 50 to 400 bp. Several landrace-specific products were identified that could be effectively used to produce landrace-specific markers for identification purposes. On average, each primer combination generated 72 amplified products that were detectable by an ABI Prism 310 DNA sequencer. The polymorphisms obtained ranged from 68.0 to 98.0%, with an average of 84.0%. The primer pairs M-ACA + P-GCC and M-ACA + P-GGA produced more polymorphic fragments than any other primer pairs and were better at differentiating landraces. The dendrogram generated by the UPGMA (unweighted pair-group method with arithmetic averaging) grouped 16 landraces into 3 clusters, mainly according to their place of collection or geographic origin. DipC1995 and Malawi5 were the most genetically related landraces. AFLP analysis provided sufficient polymorphism to determine the amount of genetic diversity and to establish genetic relationships in bambara groundnut landraces. The results will help in the formulation of marker-assisted breeding in bambara groundnut. PMID:12502264

Massawe, F J; Dickinson, M; Roberts, J A; Azam-Ali, S N

2002-12-01

284

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice ( Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo  

Microsoft Academic Search

Although the genetic diversity of rice germplasm has been well characterized globally, few studies have taken an in-depth\\u000a view of a large number of rice landraces on a local scale. To better understand the relationships between rice genetic diversity\\u000a and associated geographic and cultural factors, we collected and characterized 183 rice landraces from 18 villages along the\\u000a Bahau and Kayan

Michael J. Thomson; Nicholas R. Polato; Joko Prasetiyono; Kurniawan R. Trijatmiko; Tiur S. Silitonga; Susan R. McCouch

2009-01-01

285

Whole genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing  

PubMed Central

Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships. We show that in many instances ompA is a chimera that can be exchanged in part or whole, both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, another important diagnostic target. We have used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b.

Harris, Simon R.; Clarke, Ian N.; Seth-Smith, Helena M. B.; Solomon, Anthony W.; Cutcliffe, Lesley T.; Marsh, Peter; Skilton, Rachel J.; Holland, Martin J.; Mabey, David; Peeling, Rosanna W.; Lewis, David A.; Spratt, Brian G.; Unemo, Magnus; Persson, Kenneth; Bjartling, Carina; Brunham, Robert; de Vries, Henry J.C.; Morre, Servaas A.; Speksnijder, Arjen; Bebear, Cecile M.; Clerc, Maite; de Barbeyrac, Bertille; Parkhill, Julian; Thomson, Nicholas R.

2012-01-01

286

Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity  

PubMed Central

Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145?000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.

Esko, Tonu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Ausrele Kucinskiene, Zita; Rehnstrom, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glavac, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Kucinskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Bela; Limborska, Svetlana; Lubinski, Jan; Paolotie, Aarno; Schreiber, Stefan; Toncheva, Draga; Toniolo, Daniela; Wichmann, H-Erich; Zimprich, Alexander; Metspalu, Mait; Gasparini, Paolo; Metspalu, Andres; D'Adamo, Pio

2013-01-01

287

Invasive wisteria in the Southeastern United StateS: genetic diversity ...  

Treesearch

In this study, we use population genetic relationships to model the escape of a ... Finally, due to extensive human dispersal, there is no relationship between genetic ... Keywords: Haplotype analysis, horticulture, invasive species, sequence ...

288

The impact of global climate change on genetic diversity within populations and species.  

PubMed

Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non-neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels. PMID:23279006

Pauls, Steffen U; Nowak, Carsten; Bálint, Miklós; Pfenninger, Markus

2012-12-20

289

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.

Campbell, Michael C.; Tishkoff, Sarah A.

2010-01-01

290

Simple sequence repeat marker diversity in cassava landraces: genetic diversity and differentiation in an asexually propagated crop  

Microsoft Academic Search

Cassava ( Manihot esculenta) is an allogamous, vegetatively propagated, Neotropical crop that is also widely grown in tropical Africa and Southeast Asia. To elucidate genetic diversity and differentiation in the crop's primary and secondary centers of diversity, and the forces shaping them, SSR marker variation was assessed at 67 loci in 283 accessions of cassava landraces from Africa (Tanzania and

M. A. Fregene; M. Suarez; J. Mkumbira; H. Kulembeka; E. Ndedya; A. Kulaya; S. Mitchel; U. Gullberg; H. Rosling; A. G. O. Dixon; R. Dean; S. Kresovich

2003-01-01

291

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology  

Microsoft Academic Search

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests

Shiying Yang; Wen Pang; Gavin Ash; Jason Carling; Peter Wenzl; Eric Huttner; Xuxiao Zong; Andrzej Kilian

2006-01-01

292

Genetic diversity of Cryptosporidium spp. in captive reptiles.  

PubMed

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

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

2004-02-01

293

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.

Poirel, Laurent; Naas, Thierry; Nordmann, Patrice

2010-01-01

294

Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries.  

PubMed

Yeasts of the genus Dekkera and its anamorph Brettanomyces represent a significant spoilage issue for the global wine industry. Despite this, there is limited knowledge of genetic diversity and strain distribution within wine and winery-related environments. In this study, amplified fragment length polymorphism (AFLP) analysis was conducted on 244 Dekkera bruxellensis isolates from red wine made in 31 winemaking regions of Australia. The results indicated there were eight genotypes among the isolates, and three of these were commonly found across multiple winemaking regions. Analysis of 26S rRNA gene sequences provided further evidence of three common, conserved groups, whereas a phylogeny based upon the AFLP data demonstrated that the most common D. bruxellensis genotype (I) in Australian red wine was highly divergent from the D. bruxellensis type strain (CBS 74). PMID:17233769

Curtin, Chris D; Bellon, Jennifer R; Henschke, Paul A; Godden, Peter W; de Barros Lopes, Miguel A

2007-01-15

295

Genetic diversity of Flavobacterium psychrophilum isolated from rainbow trout in France: predominance of a clonal complex.  

PubMed

Flavobacterium psychrophilum is the causative agent of "bacterial cold water disease" and "rainbow trout fry syndrome" in salmonid farming worldwide. These diseases, especially rainbow trout fry syndrome, are among the main hazards for French aquaculture. In this study, a multilocus sequence typing approach (MLST) was used to evaluate the genetic diversity of this bacterium. Seven housekeeping genes in a set of 66 isolates were investigated. They were recently collected from rainbow trout during clinical episodes in French farms from the two main geographical areas of production. A total of 5808 bp of sequence were analyzed for each isolate and showed relatively low levels of gene (H=0.4313) and nucleotide (?×100=0.31%) diversities. MLST identified 15 sequence types (STs), of which 14 have never been described. eBURST analysis separated the 15 STs in one clonal complex of 8 genetically related STs (with ST2 as founder) and 7 singletons. Genetic diversity was largely due to recombination, as demonstrated by a pairwise homoplasy index (PHI=5.35×10(-9)) significantly different from zero (p<0.05). The evolution of standardized association index (I(A)(S)) (all isolates: 0.6088, p<0.05; single representative of STs: 0.4567, p<0.05; and clusters of STs: 0.084, p>0.05), showed an epidemic structure of the population. These results emphasized the expansion of a limited number of dominant genetic variants in French clinical F. psychrophilum isolates from a single host species, with no geographic relationships. PMID:22871298

Siekoula-Nguedia, C; Blanc, G; Duchaud, E; Calvez, S

2012-07-20

296

Opposites attract or attack? The moderating role of diversity climate in the team diversity-interpersonal aggression relationship.  

PubMed

This study embraced a unit-level diversity perspective to examine interpersonal aggression, as experienced or witnessed by individual team members. Specifically, our aim was to explore the moderating role of a unit's diversity climate in the link between unit-level surface diversity in terms of ethnicity, sex, age, and tenure, and individual-level perceptions of interpersonal aggression. We tested our hypotheses with 30 nursing units using the Mixed-Linear Model procedure appropriate for nested samples. Results demonstrated that diversity climate moderated the relationships between tenure and ethnic unit diversity and interpersonal aggression, experienced or witnessed among individual team members. Moreover, regardless of the level of diversity climate, age diversity was positively linked to interpersonal aggression, whereas sex diversity was negatively linked to it. These findings imply that the unit's context affects interpersonal aggression and provides important theoretical and practical implications to proactively prevent interpersonal aggression. (PsycINFO Database Record (c) 2013 APA, all rights reserved). PMID:24099164

Drach-Zahavy, Anat; Trogan, Revital

2013-10-01

297

Genetic diversity of ITS sequences of Bursaphelenchus xylophilus.  

PubMed

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

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

2012-12-19

298

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.

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

2011-01-01

299

Genetic diversity of Toxoplasma gondii in animals and humans  

PubMed Central

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

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

2009-01-01

300

Genetic diversity of Babesia bovis in virulent and attenuated strains.  

PubMed

The aim of this study was to compare the genetic diversity of the single copy Bv80 gene sequences of Babesia bovis in populations of attenuated and virulent parasites. PCR/ RT-PCR followed by cloning and sequence analyses of 4 attenuated and 4 virulent strains were performed. Multiple fragments in the range of 420 to 744 bp were amplified by PCR or RT-PCR. Cloning of the PCR fragments and sequence analyses revealed the presence of mixed subpopulations in either virulent or attenuated parasites with a total of 19 variants with 12 different sequences that differed in number and type of tandem repeats. High levels of intra- and inter-strain diversity of the Bv80 gene, with the presence of mixed populations of parasites were found in both the virulent field isolates and the attenuated vaccine strains. In addition, during the attenuation process, sequence analyses showed changes in the pattern of the parasite subpopulations. Despite high polymorphism found by sequence analyses, the patterns observed and the number of repeats, order, or motifs found could not discriminate between virulent field isolates and attenuated vaccine strains of the parasite. PMID:22075976

Mazuz, M L; Molad, T; Fish, L; Leibovitz, B; Wolkomirsky, R; Fleiderovitz, L; Shkap, V

2011-11-11

301

Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants.  

PubMed

Multi-locus sequence typing was performed on 1003 Campylobacter jejuni isolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasture vs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206. PMID:21134320

Grove-White, D H; Leatherbarrow, A J H; Cripps, P J; Diggle, P J; French, N P

2010-12-07

302

Molecular characterization and population genetic diversity of Limonium sinense based on nuclear ribosomal DNA and ISSR.  

PubMed

The single nucleotide polymorphism (SNP) and amplification refractory mutation system (ARMS) have been applied to authenticate Limonium species and their corresponding herb samples. One species specific primer was designed and the amplification product is 200 bp (Limonium sinense) by using this primer. No band was observed with other Limonium species. The phylogenetic relationship of Limonium species were studied using ribosomal DNA ITS and the adulterants (L. bicolor, L. aureum and L. wrightii) were clustered with L. sinense in NJ tree. Inter simple sequence repeat (ISSR) was used to assess genetic diversity and population structure of L. sinense and a high level of genetic diversity was detected (H(E) = 0.2573, PPB = 85.71%) with POPGENE. Based on AMOVA analysis, there was moderate variation between pairs of populations with phi(ST) from 0.1744 to 0.5131 and on average 28.81% of the genetic variation occurred among populations. Five main clusters were shown in UPGMA dendrogram using TFPGA. The results showed that SNP and ARMS could be used to authenticate not only Limonium species but related herbs on rDNA internal transcribed spacer region. Possible strategies should be implemented for conservation of this endemic herb. PMID:24159804

Ding, G; Zhang, D; Yu, Y; Zhang, B; Zhao, L

2013-05-01

303

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

304

Genetic diversity of Toxoplasma gondii isolates from Ethiopian feral cats.  

PubMed

Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioassays in mice from tissues and feces of 27 cats from Ethiopia. Viable T. gondii was isolated from hearts of 26 cats, feces alone of 1 cat, and feces and tissues of 6 cats; in total there were 33 isolates. Genotyping was performed on DNA from cell-cultured derived T. gondii tachyzoites and by using 10 PCR-restriction fragment length polymorphism markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Four genotypes were recognized, including ToxoDB #1 (Type II clonal, nine isolates), ToxoDB #2 (Type III, five isolates), Toxo DB #3 (Type II variant, ten isolates), and ToxoDB #20 (nine isolates). Of interest is the isolation of different genotypes from tissues and feces of two cats, suggesting re-infection or mixed strain T. gondii infection. These findings are of epidemiological significance with respect to shedding of oocysts by cats. This is the first report of genotyping of T. gondii from any host in Ethiopia. PMID:23411374

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

2013-01-24

305

Genetic diversity and tetracycline resistance genes of Histophilus somni.  

PubMed

Nasal swabs were collected at three time points from 2378 calves in four feedlots and cultured for Histophilus somni to assess genetic relatedness and tetracycline resistance. The proportions of animals carrying tetracycline resistant isolates were 0.32% at arrival, 14.82% at interim, and 0.80% at exit. The 606 H. somni isolates recovered were compared by pulsed-field gel electrophoresis (PFGE), screened for the presence of plasmids, and assessed for the tetracycline resistance genes tet(A), tet(B), tet(C), tet(E), tet(G), tet(H), tet(K), tet(L), tet(M) and tet(O) using multiplex polymerase chain reaction. Most of the isolates (98.6%) belonged to one of seven PFGE clusters (A-G) of closely related profiles with 77.7% of the isolates belonging to clusters C and D. Clusters A, B and E were associated with a higher proportion of tetracycline susceptible isolates. Genetic diversity of the isolates was highest at entry in the feedlot and lowest after the period when the animals received in-feed chlortetracycline (interim samples). Clusters A and E were more prominently represented at exit from the feedlot than other clusters. All resistant strains harboured the gene tet(H) while no other tetracycline resistance genes and no plasmids were detected with the methodology employed. It appears that genetic variability in H. somni in Alberta feedlots is low, dissemination likely occurs by clonal expansion, and resistance to tetracyclines is mediated by the tet(H) encoded efflux pump. Pulsotypes associated with tetracycline susceptible strains appear more common at exit suggesting that the in-feed oxytetracycline included throughout the feeding period is not sufficient to exert selective pressure for resistant strains. PMID:21482045

D'Amours, Geneviève H; Ward, Tracy I; Mulvey, Michael R; Read, Ronald R; Morck, Douglas W

2011-03-16

306

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.

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

307

Genetic diversity revealed by single nucleotide polymorphism markers in a worldwide germplasm collection of durum wheat.  

PubMed

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

2013-03-28

308

Genetic Relationships Between Selection for Growth and Reproductive Effectiveness  

Microsoft Academic Search

The domestic and international poultry industries have gone through many changes over the last 50 yr. One constant in the meat-type poultry industry has been the emphasis on genetic improvement of growth. Using lines from a double, divergent selection experiment, data are presented on the genetic relationships between growth to different ages and reproductive parameters. During the last three genera-

G. F. BARBATO

309

The effect of inoculum dose on the genetic diversity detected within Helicoverpa armigera nucleopolyhedrovirus populations.  

PubMed

Environmental and infection variables may affect the genetic diversity of baculovirus populations. In this study, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying the effects of a key infection variable, inoculum dose, on the genetic diversity within nucleopolyhedrovirus populations. Diversity and equitability indices were calculated from DNA polymerase-specific denaturing gradient gel electrophoresis profiles obtained from individual H. armigera neonate larvae inoculated with either an LD5 or LD95 of HearNPV. Although the genetic diversity detected in larvae treated with an LD95 was not statistically different from the diversity detected in the HearNPV inoculum samples, there was a statistically significant difference in the genetic diversity detected in the LD5-inoculated larvae compared with the genetic diversity detected in the HearNPV samples used for the inoculations. The study suggests that inoculum dose needs to be considered carefully in experiments that evaluate HearNPV genetic diversity or in studies where differences in genetic diversity may have phenotypic consequences. PMID:23929831

Baillie, Vicky Lynne; Bouwer, Gustav

2013-08-08

310

Genetic diversity and genetic structure of adult and buried seed populations of Betula maximowicziana in mixed and post-fire stands  

Microsoft Academic Search

The genetic diversity and genetic structure of plant populations are influenced by processes of regeneration. Assessing the genetic composition of populations regenerated by different modes is important for successful forest management and conservation. In this study, we compared the genetic diversity and genetic structure of six populations in mixed stands with those of four post-fire stands of the noble hardwood

Kentaro Uchiyama; Susumu Goto; Yoshiaki Tsuda; Yasuo Takahashi; Yuji Ide

2006-01-01

311

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

312

Genetic diversity patterns in Phragmites australis at the population, regional and continental scales  

Microsoft Academic Search

Genetic diversity, population structure and interrelationships were investigated in eight populations of the common reed, Phragmites australis, in the Po Plain, Italy, by means of amplified fragments length polymorphisms (AFLPs) and random amplified polymorphic DNAs (RAPDs). Patterns of genetic diversity were analysed in relation to size, age and degree of human impact in the wetlands and compared with that of

Carla Lambertini; Mats H. G. Gustafsson; Jane Frydenberg; Maria Speranza; Hans Brix

2008-01-01

313

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

314

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

315

Effects of Life History Traits on Genetic Diversity in Plant Species  

Microsoft Academic Search

Seven two-trait combinations (e.g. breeding system and seed dispersal mechanism) of five life history characteristics were used to analyse interspecific variation in the level and distribution of allozyme genetic diversity in seed plants. Highly significant differences were seen among categories for all seven comparisons. Life form and breeding system had highly significant influences on genetic diversity and its distribution. Regardless

J. L. Hamrick; M. J. W. Godt

1996-01-01

316

Genetic Structure and Diversity Among Maize Inbred Lines as Inferred From DNA Microsatellites  

Microsoft Academic Search

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in

Kejun Liu; Major Goodman; Spencer Muse; J. Stephen Smith; Ed Buckler; John Doebley

2003-01-01

317

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

318

Genetic diversity, inbreeding and breeding practices in dogs: Results from pedigree analyses  

Microsoft Academic Search

Pedigree analysis constitutes a classical approach for the study of the evolution of genetic diversity, genetic structure, history and breeding practices within a given breed. As a consequence of selection pressure, management in closed populations and historical bottlenecks, many dog breeds have experienced considerable inbreeding and show (on the basis of a pedigree approach) comparable diversity loss compared to other

Grégoire Leroy

2011-01-01

319

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

2011-12-29

320

Mitochondrial DNA diversity, origin, and phylogenic relationships of three Chinese large-fat-tailed sheep breeds  

Microsoft Academic Search

China is abundant of sheep genetic resources. A total of 55 sequences containing the Ovis aries mtDNA D-loop of three large-fat-tailed sheep breeds, named Lanzhou, Tong, and Han were retrieved from GenBank to investigate their\\u000a genetic diversity, origin, and phylogenetic evolution. The results showed that the sheep breeds in our study proved to be\\u000a extremely diverse, the average haplotype diversity

Yongju Zhao; Erhu Zhao; Nanyang Zhang; Chaowei Duan

2011-01-01

321

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

PubMed

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

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

2007-09-01

322

Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding*  

PubMed Central

The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China.

Wang, Jun-mei; Yang, Jian-ming; Zhu, Jing-huan; Jia, Qiao-jun; Tao, Yue-zhi

2010-01-01

323

Genetic diversity of Brassica napus L. Germplasm from China and Europe assessed by some agronomically important characters  

Microsoft Academic Search

Summary  The genetic diversity and relationships among 63 rapeseed accessions, including 34 Chinese, 22 Czech, 2 Swedish, 2 German,\\u000a one French and 2 Canadian accessions, were evaluated by nine agronomically important characters in the field at Yangling,\\u000a Shaanxi, China. Significant differences between Chinese and European group in plant height, setting position of the first\\u000a primary branch, number of siliques of the

Shengwu Hu; Chengyu Yu; Huixian Zhao; Genlou Sun; Suolao Zhao; Miroslava Vyvadilova; Vratislav Kucera

2007-01-01

324

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

325

Genetic Diversity in RNA Virus Quasispecies Is Controlled by Host-Virus Interactions  

Microsoft Academic Search

Many RNA viruses have genetically diverse populations known as quasispecies. Important biological char- acteristics may be related to the levels of diversity in the quasispecies (quasispecies cloud size), including adaptability and host range. Previous work using Tobacco mosaic virus and Cucumber mosaic virus indicated that evolutionarily related viruses have very different levels of diversity in a common host. The quasispecies

WILLIAM L. SCHNEIDER; MARILYN J. ROOSSINCK

2001-01-01

326

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

327

Genetic Diversity Among Botulinum Neurotoxin Producing Clostridial Strains  

SciTech Connect

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore forming rod-shaped bacteria which have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and even death in humans and various other animal species. A collection of 174 C. botulinum strains were examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT A-G). Analysis of the16S rRNA sequences confirmed earlier reports of at least four distinct genomic backgrounds (Groups I-IV) each of which has independently acquired one or more BoNT serotypes through horizontal gene transfer. AFLP analysis provided higher resolution, and can be used to further subdivide the four groups into sub-groups. Sequencing of the BoNT genes from serotypes A, B and E in multiple strains confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes, and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven serotypes of BoNT were compared and show varying degrees of interrelatedness and recombination as has been previously noted for the NTNH gene which is linked to BoNT. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for treatment of botulism.

Hill, K K; Smith, T J; Helma, C H; Ticknor, L O; Foley, B T; Svennson, R T; Brown, J L; Johnson, E A; Smith, L A; Okinaka, R T; Jackson, P J; Marks, J D

2006-07-06

328

Genetic Diversity of the Allodeterminant alr2 in Hydractinia symbiolongicarpus  

PubMed Central

Hydractinia symbiolongicarpus, a colonial cnidarian (class Hydrozoa) epibiont on hermit crab shells, is well established as a model for genetic studies of allorecognition. Recently, two linked loci, allorecognition (alr) 1 and alr2, were identified by positional cloning and shown to be major determinants of histocompatibility. Both genes encode putative transmembrane proteins with hypervariable extracellular domains similar to immunoglobulin (Ig)-like domains. We sought to characterize the naturally occurring variation at the alr2 locus and to understand the origins of this molecular diversity. We examined full-length cDNA coding sequences derived from a sample of 21 field-collected colonies, including 18 chosen haphazardly and two laboratory reference strains. Of the 35 alleles recovered from the 18 unbiased samples, 34 encoded unique gene products. We identified two distinct structural classes of alleles that varied over a large central region of the gene but both possessed highly polymorphic extracellular domains I, similar to an Ig-like V-set domain. The discovery of structurally chimeric alleles provided evidence that interallelic recombination may contribute to alr2 variation. Comparisons of the genomic region encompassing alr2 from two field-derived haplotypes and one laboratory reference sequence revealed a history of structural variation at the haplotype level as well. Maintenance of large numbers of equally rare alleles in a natural population is a hallmark of negative frequency–dependent selection and is expected to produce high levels of heterozygosity. The observed alr2 allelic diversity is comparable with that found in immune recognition molecules such as human leukocyte antigens, B cell Igs, or natural killer cell Ig-like receptors.

Rosengarten, Rafael D.; Moreno, Maria A.; Lakkis, Fadi G.; Buss, Leo W.; Dellaporta, Stephen L.

2011-01-01

329

Genetic diversity of the allodeterminant alr2 in Hydractinia symbiolongicarpus.  

PubMed

Hydractinia symbiolongicarpus, a colonial cnidarian (class Hydrozoa) epibiont on hermit crab shells, is well established as a model for genetic studies of allorecognition. Recently, two linked loci, allorecognition (alr) 1 and alr2, were identified by positional cloning and shown to be major determinants of histocompatibility. Both genes encode putative transmembrane proteins with hypervariable extracellular domains similar to immunoglobulin (Ig)-like domains. We sought to characterize the naturally occurring variation at the alr2 locus and to understand the origins of this molecular diversity. We examined full-length cDNA coding sequences derived from a sample of 21 field-collected colonies, including 18 chosen haphazardly and two laboratory reference strains. Of the 35 alleles recovered from the 18 unbiased samples, 34 encoded unique gene products. We identified two distinct structural classes of alleles that varied over a large central region of the gene but both possessed highly polymorphic extracellular domains I, similar to an Ig-like V-set domain. The discovery of structurally chimeric alleles provided evidence that interallelic recombination may contribute to alr2 variation. Comparisons of the genomic region encompassing alr2 from two field-derived haplotypes and one laboratory reference sequence revealed a history of structural variation at the haplotype level as well. Maintenance of large numbers of equally rare alleles in a natural population is a hallmark of negative frequency-dependent selection and is expected to produce high levels of heterozygosity. The observed alr2 allelic diversity is comparable with that found in immune recognition molecules such as human leukocyte antigens, B cell Igs, or natural killer cell Ig-like receptors. PMID:20966116

Rosengarten, Rafael D; Moreno, Maria A; Lakkis, Fadi G; Buss, Leo W; Dellaporta, Stephen L

2010-10-21

330

Genetic Diversity among Botulinum Neurotoxin-Producing Clostridial Strains?  

PubMed Central

Clostridium botulinum is a taxonomic designation for many diverse anaerobic spore-forming rod-shaped bacteria that have the common property of producing botulinum neurotoxins (BoNTs). The BoNTs are exoneurotoxins that can cause severe paralysis and death in humans and other animal species. A collection of 174 C. botulinum strains was examined by amplified fragment length polymorphism (AFLP) analysis and by sequencing of the 16S rRNA gene and BoNT genes to examine the genetic diversity within this species. This collection contained representatives of each of the seven different serotypes of botulinum neurotoxins (BoNT/A to BoNT/G). Analysis of the16S rRNA gene sequences confirmed previous identifications of at least four distinct genomic backgrounds (groups I to IV), each of which has independently acquired one or more BoNT genes through horizontal gene transfer. AFLP analysis provided higher resolution and could be used to further subdivide the four groups into subgroups. Sequencing of the BoNT genes from multiple strains of serotypes A, B, and E confirmed significant sequence variation within each serotype. Four distinct lineages within each of the BoNT A and B serotypes and five distinct lineages of serotype E strains were identified. The nucleotide sequences of the seven toxin genes of the serotypes were compared and showed various degrees of interrelatedness and recombination, as was previously noted for the nontoxic nonhemagglutinin gene, which is linked to the BoNT gene. These analyses contribute to the understanding of the evolution and phylogeny within this species and assist in the development of improved diagnostics and therapeutics for the treatment of botulism.

Hill, K. K.; Smith, T. J.; Helma, C. H.; Ticknor, L. O.; Foley, B. T.; Svensson, R. T.; Brown, J. L.; Johnson, E. A.; Smith, L. A.; Okinaka, R. T.; Jackson, P. J.; Marks, J. D.

2007-01-01

331

Genetic diversity of perch rhabdoviruses isolates based on the nucleoprotein and glycoprotein genes.  

PubMed

Despite the increasing impact of rhabdoviruses in European percid farming, the diversity of the viral populations is still poorly investigated. To address this issue, we sequenced the partial nucleoprotein (N) and complete glycoprotein (G) genes of nine rhabdoviruses isolated from perch (Perca fluviatilis) between 1999 and 2010, mostly from France, and analyzed six of them by immunofluorescence antibody test (IFAT). Using two rabbit antisera raised against either the reference perch rhabdovirus (PRhV) isolated in 1980 or the perch isolate R6146, two serogroups were distinguished. Meanwhile, based on partial N and complete G gene analysis, perch rhabdoviruses were divided into four genogroups, A-B-D and E, with a maximum of 32.9% divergence (G gene) between isolates. A comparison of the G amino acid sequences of isolates from the two identified serogroups revealed several variable regions that might account for antigenic differences. Comparative analysis of perch isolates with other rhabdoviruses isolated from black bass, pike-perch and pike showed some strong phylogenetic relationships, suggesting cross-host transmission. Similarly, striking genetic similarities were shown between perch rhabdoviruses and isolates from other European countries and various ecological niches, most likely reflecting the circulation of viruses through fish trade as well as putative transfers from marine to freshwater fish. Phylogenetic relationships of the newly characterized viruses were also determined within the family Rhabdoviridae. The analysis revealed a genetic cluster containing only fish viruses, including all rhabdoviruses from perch, as well as siniperca chuatsi rhabdovirus (SCRV) and eel virus X (EVEX). This cluster was distinct from the one represented by spring viraemia of carp vesiculovirus (SVCV), pike fry rhabdovirus (PFRV) and mammalian vesiculoviruses. The new genetic data provided in the present study shed light on the diversity of rhabdoviruses infecting perch in France and support the hypothesis of circulation of these viruses between other hosts and regions within Europe. PMID:21927897

Talbi, Chiraz; Cabon, Joelle; Baud, Marine; Bourjaily, Maya; de Boisséson, Claire; Castric, Jeannette; Bigarré, Laurent

2011-09-17

332

Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13  

PubMed Central

Background Salmonella enterica serovar Enteritidis has emerged as a significant foodborne pathogen throughout the world and is commonly characterized by phage typing. In Canada phage types (PT) 4, 8 and 13 predominate and in 2005 a large foodborne PT13 outbreak occurred in the province of Ontario. The ability to link strains during this outbreak was difficult due to the apparent clonality of PT13 isolates in Canada, as there was a single dominant pulsed-field gel electrophoresis (PFGE) profile amongst epidemiologically linked human and food isolates as well as concurrent sporadic strains. The aim of this study was to perform comparative genomic hybridization (CGH), DNA sequence-based typing (SBT) genomic analyses, plasmid analyses, and automated repetitive sequence-based PCR (rep-PCR) to identify epidemiologically significant traits capable of subtyping S. Enteritidis PT13. Results CGH using an oligonucleotide array based upon chromosomal coding sequences of S. enterica serovar Typhimurium strain LT2 and the Salmonella genomic island 1 successfully determined major genetic differences between S. Typhimurium and S. Enteritidis PT13, but no significant strain-to-strain differences were observed between S. Enteritidis PT13 isolates. Individual loci (safA and fliC) that were identified as potentially divergent in the CGH data set were sequenced in a panel of S. Enteritidis strains, and no differences were detected between the PT13 strains. Additional sequence-based typing was performed at the fimA, mdh, manB, cyaA, citT, caiC, dmsA, ratA and STM0660 loci. Similarly, no diversity was observed amongst PT13 strains. Variation in plasmid content between PT13 strains was observed, but macrorestriction with BglII did not identify further differences. Automated rep-PCR patterns were variable between serovars, but S. Enteritidis PT13 strains could not be differentiated. Conclusion None of the methods identified any significant variation between PT13 strains. Greater than 11,300 base pairs of sequence for each of seven S. Enteritidis PT13 strains were analyzed without detecting a single polymorphic site, although diversity between different phage types of S. Enteritidis was observed. These data suggest that Canadian S. Enteritidis PT13 strains are highly related genetically.

Olson, Adam B; Andrysiak, Ashleigh K; Tracz, Dobryan M; Guard-Bouldin, Jean; Demczuk, Walter; Ng, Lai-King; Maki, Anne; Jamieson, Frances; Gilmour, Matthew W

2007-01-01

333

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

334

Genetic diversity of Phytophthora infestans in the Northern Andean region  

PubMed Central

Background Phytophthora infestans (Mont.) de Bary, the causal agent of potato late blight, is responsible for tremendous crop losses worldwide. Countries in the northern part of the Andes dedicate a large proportion of the highlands to the production of potato, and more recently, solanaceous fruits such as cape gooseberry (Physalis peruviana) and tree tomato (Solanum betaceum), all of which are hosts of this oomycete. In the Andean region, P. infestans populations have been well characterized in Ecuador and Peru, but are poorly understood in Colombia and Venezuela. To understand the P. infestans population structure in the Northern part of the Andes, four nuclear regions (ITS, Ras, ?-tubulin and Avr3a) and one mitochondrial (Cox1) region were analyzed in isolates of P. infestans sampled from different hosts in Colombia and Venezuela. Results Low genetic diversity was found within this sample of P. infestans isolates from crops within several regions of Colombia and Venezuela, revealing the presence of clonal populations of the pathogen in this region. We detected low frequency heterozygotes, and their distribution patterns might be a consequence of a high migration rate among populations with poor effective gene flow. Consistent genetic differentiation exists among isolates from different regions. Conclusions The results here suggest that in the Northern Andean region P. infestans is a clonal population with some within-clone variation. P. infestans populations in Venezuela reflect historic isolation that is being reinforced by a recent self-sufficiency of potato seeds. In summary, the P. infestans population is mainly shaped by migration and probably by the appearance of variants of key effectors such as Avr3a.

2011-01-01

335

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

PubMed

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

John Wallace, R

2008-05-01

336

Genetic relationships among breeds of beef cattle  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

337

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

338

Asymmetric gene flow and the evolutionary maintenance of genetic diversity in small, peripheral Atlantic salmon populations  

Microsoft Academic Search

Small populations may be expected to harbour less genetic variation than large populations, but the relation between census\\u000a size (N), effective population size (N\\u000a e), and genetic diversity is not well understood. We compared microsatellite variation in four small peripheral Atlantic salmon\\u000a populations from the Iberian peninsula and three larger populations from Scotland to test whether genetic diversity was related

Sofía Consuegra; Eric Verspoor; David Knox; Carlos García de Leániz

2005-01-01

339

Genetic Diversity and Variation Among Botanical Varieties of Old Portuguese Wheat Cultivars Revealed by ISSR Assays  

Microsoft Academic Search

Inter-simple sequence repeats (ISSRs) were used for genetic diversity analyses of an Old Portuguese wheat collection. Eighteen\\u000a primers produced 96.3 and 98.5% of ISSR polymorphism in bread and durum wheat cultivars, respectively. The unweighted pair\\u000a group method with arithmetical averages (UPGMA) phenogram clearly split all cultivars based on their species\\/ploidy, reflecting\\u000a a defined genetic structure. ISSRs revealed high genetic diversity

Ana Carvalho; José Lima-Brito; Benvindo Maçãs; Henrique Guedes-Pinto

2009-01-01

340

Multiple-population versus hierarchical conifer breeding programs: a comparison of genetic diversity levels  

Microsoft Academic Search

Advanced-generation domestication programs for forest-tree species has raised some concerns about the maintenance of genetic diversity in forest-tree breeding programs. Genetic diversity in natural stands was compared with two genetic conservation options for a third-generation elite Pinus taeda breeding population. The breeding population was subdivided either on the basis of geographic origin and selection goals (multiple-population or MPBS option) or

C. G. Williams; J. L. Hamrick; P. O. Lewis

1995-01-01

341

Genetic Diversity and the Reproductive System in Related Species of Antirrhinum  

PubMed Central

• Background and Aims Seven related species of Antirrhinum (A. siculum, A. majus, A. latifolium, A. linkianum, A. litigiosum, A. cirrhigherum and A. tortuosum) were studied in order to compare levels of genetic variation and its partitioning in them, and to check relationships between genetic patterns and the reproductive system. • Methods Eight hundred and fifty-one plants were screened for variability at 13 allozyme loci by means of horizontal starch gel electrophoresis. Parameters of genetic diversity and its partitioning, the inbreeding coefficient as well as an indirect estimate of gene flow based on the equation: Nm = (1 ? GST)/4GST, were calculated. • Key Results Genetic variability in A. siculum was found to be the lowest known in the genus. Mean values of FIT and FIS were mostly positive and not significantly different from zero. Population differentiation (FST) ranged between 6·1 in A. tortuosum and 17·6 in A. linkianum. The inbreeding coefficient within populations ranged between FIS = ?0·5 in A. tortuosum and FIS = 1 in A. siculum. Estimates of gene flow ranged between Nm = 15 in A. majus (considered as very high) to Nm = 0·42 in A. siculum (considered as low). • Conclusions Correlation was found between levels of diversity and differentiation on one hand, and the reproductive system of the studied taxa on the other. Striking differences among species in the inbreeding coefficient (FIS) show different reproductive systems, which mostly support previous reports. Strategies for the conservation of A. siculum are recommended, such as preservation of natural populations as well as ex situ preservation of seeds from different populations.

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

2006-01-01

342

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.

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

1995-01-01

343

Dilated cardiomyopathy: the complexity of a diverse genetic architecture.  

PubMed

Remarkable progress has been made in understanding the genetic basis of dilated cardiomyopathy (DCM). Rare variants in >30 genes, some also involved in other cardiomyopathies, muscular dystrophy, or syndromic disease, perturb a diverse set of important myocardial proteins to produce a final DCM phenotype. Large, publicly available datasets have provided the opportunity to evaluate previously identified DCM-causing mutations, and to examine the population frequency of sequence variants similar to those that have been observed to cause DCM. The frequency of these variants, whether associated with dilated or hypertrophic cardiomyopathy, is greater than estimates of disease prevalence. This mismatch might be explained by one or more of the following possibilities: that the penetrance of DCM-causing mutations is lower than previously thought, that some variants are noncausal, that DCM prevalence is higher than previously estimated, or that other more-complex genomics underlie DCM. Reassessment of our assumptions about the complexity of the genomic and phenomic architecture of DCM is warranted. Much about the genomic basis of DCM remains to be investigated, which will require comprehensive genomic studies in much larger cohorts of rigorously phenotyped probands and family members than previously examined. PMID:23900355

Hershberger, Ray E; Hedges, Dale J; Morales, Ana

2013-07-30

344

Parasites mediate the relationship between host diversity and disturbance frequency  

Microsoft Academic Search

Patterns of community and population diversity are likely to be dependent on interactions between ecological variables. Here we address how two important ecological variables - extrinsic periodic mortality events (disturbances) and the presence of obligate-killing parasites - interact to affect the diversity of niche-specialist genotypes in laboratory populations of the bacterium Pseudomonas fluorescens. Consistent with previous studies, diversity was maximized

Andrew D. Morgan; Angus Buckling

2004-01-01

345

Anthropogenic alterations of genetic diversity within tree populations: Implications for forest ecosystem resilience  

Microsoft Academic Search

Healthy forests provide many of the essential ecosystem services upon which all life depends. Genetic diversity is an essential component of long-term forest health because it provides a basis for adaptation and resilience to environmental stress and change. In addition to natural processes, numerous anthropogenic factors deplete forest genetic resources. Genetic losses could be particularly consequential now because robust resilience

Paul G. Schaberg; Donald H. DeHayes; Gary J. Hawley; Samuel E. Nijensohn

2008-01-01

346

Invasion success and genetic diversity of introduced populations of guppies Poecilia reticulata in Australia  

Microsoft Academic Search

High genetic diversity is thought to characterize successful invasive species, as the potential to adapt to new environments is enhanced and inbreeding is reduced. In the last century, guppies, Poecilia reticulata, repeatedly invaded streams in Australia and elsewhere. Quan- titative genetic studies of one Australian guppy population have demonstrated high addi- tive genetic variation for autosomal and Y-linked morphological traits.

ANNA K. LINDHOLM; FELIX BREDEN; HEATHER J. ALEXANDER; WOON-KHIONG CHAN; SUMITA G. THAKURTA; ROBERT BROOKS

2005-01-01

347

High genetic diversity in a rare and endangered sunflower as compared to a common congener  

Microsoft Academic Search

Determining the genetic structure of isolated or fragmented species is of critical importance when planning a suitable conservation strategy. In this study, we use nuclear and chloroplast SSRs (simple sequence repeats) to investigate the population genetics of an extremely rare sunflower, Helianthus verticillatus Small, which is known from only three locations in North America. We investigated levels of genetic diversity

J. R. ELLIS; C. H. PASHLEY; J. M. BURKE; D. E. M C CAULEY

2006-01-01

348

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

349

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

350

A social capital explanation of the relationship between functional diversity and group performance  

Microsoft Academic Search

Purpose – Functional diversity research has resulted in equivocal findings for group performance suggesting the need for theoretical clarification. A review of previous functional diversity research indicates that high quality productive relationships are a key determinant in the performance of cognitively diverse groups. A theoretical framework is provided that demonstrates that assets embedded in the social structure of group member

W. Randy Evans; Charles M. Carson

2005-01-01

351

Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry.  

PubMed

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

2010-08-13

352

Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures  

Microsoft Academic Search

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such

Jörn Bennewitz; Juha Kantanen; Ilma Tapio; Meng Hua Li; Ernst Kalm; Johanna Vilkki; Innokentyi Ammosov; Zoya Ivanova; Tatyana Kiselyova; Ruslan Popov; Theo HE Meuwissen

2006-01-01

353

Genetic diversity in cultivated carioca common beans based on molecular marker analysis  

PubMed Central

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Kupper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sergio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

2011-01-01

354

Genetic diversity of expressed Plasmodium falciparum var genes from Tanzanian children with severe malaria  

PubMed Central

Background Severe malaria has been attributed to the expression of a restricted subset of the var multi-gene family, which encodes for Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 mediates cytoadherence and sequestration of infected erythrocytes into the post-capillary venules of vital organs such as the brain, lung or placenta. var genes are highly diverse and can be classified in three major groups (ups A, B and C) and two intermediate groups (B/A and B/C) based on the genomic location, gene orientation and upstream sequences. The genetic diversity of expressed var genes in relation to severity of disease in Tanzanian children was analysed. Methods Children with defined severe (SM) and asymptomatic malaria (AM) were recruited. Full-length var mRNA was isolated and reversed transcribed into var cDNA. Subsequently, the DBL and N-terminal domains, and up-stream sequences were PCR amplified, cloned and sequenced. Sequences derived from SM and AM isolates were compared and analysed. Results The analysis confirmed that the var family is highly diverse in natural Plasmodium falciparum populations. Sequence diversity of amplified var DBL-1? and upstream regions showed minimal overlap among isolates, implying that the var gene repertoire is vast and most probably indefinite in endemic areas. var DBL-1? sequences from AM isolates were more diverse with more singletons found (p<0.05) than those from SM infections. Furthermore, few var DBL-1? sequences from SM patients were rare and restricted suggesting that certain PfEMP1 variants might induce severe disease. Conclusions The genetic sequence diversity of var genes of P. falciparum isolates from Tanzanian children is large and its relationship to disease severity has been studied. Observed differences suggest that different var genes might have fundamentally different roles in the host-parasite interaction. Further research is required to examine clear disease-associations of var gene subsets in different geographical settings. The importance of very strict clinical definitions and appropriate large control groups needs to be emphasized for future studies on disease associations of PfEMP1.

2012-01-01

355

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

Microsoft Academic Search

The resilience of Symbiodinium harboured by corals is dependent on the genetic diversity and extent of connectivity among reef populations. This study presents\\u000a genetic analyses of Great Barrier Reef (GBR) populations of clade C Symbiodinium hosted by the alcyonacean coral, Sinularia flexibilis. Allelic variation at four newly developed microsatellite loci demonstrated that Symbiodinium populations are genetically differentiated at all spatial scales

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

2009-01-01

356

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.

Ikegami, Tetsuro

2013-01-01

357

Metabolism of sugars by genetically diverse species of oral Leptotrichia.  

PubMed

Leptotrichia buccalis ATCC 14201 is a gram-negative, anaerobic rod-shaped bacterium resident in oral biofilm at the tooth surface. The sequenced genome of this organism reveals three contiguous genes at loci: Lebu_1525, Lebu_1526 and Lebu_1527. The translation products of these genes exhibit significant homology with phospho-?-glucosidase (Pagl), a regulatory protein (GntR) and a phosphoenol pyruvate-dependent sugar transport protein (EIICB), respectively. In non-oral bacterial species, these genes comprise the sim operon that facilitates sucrose isomer metabolism. Growth studies showed that L. buccalis fermented a wide variety of carbohydrates, including four of the five isomers of sucrose. Growth on the isomeric disaccharides elicited expression of a 50-kDa polypeptide comparable in size to that encoded by Lebu_1525. The latter gene was cloned, and the expressed protein was purified to homogeneity from Escherichia coli TOP10 cells. In the presence of two cofactors, NAD(+) and Mn(2+) ions, the enzyme readily hydrolyzed p-nitrophenyl-?-glucopyranoside 6-phosphate (pNP?G6P), a chromogenic analogue of the phosphorylated isomers of sucrose. By comparative sequence alignment, immunoreactivity and signature motifs, the enzyme can be assigned to the phospho-?-glucosidase (Pagl) clade of Family 4 of the glycosyl hydrolase super family. We suggest that the products of Lebu_1527 and Lebu_1525, catalyze the phosphorylative translocation and hydrolysis of sucrose isomers in L. buccalis, respectively. Four genetically diverse, but 16S rDNA-related, species of Leptotrichia have recently been described: L. goodfellowii, L. hofstadii, L. shahii and L. wadei. The phenotypic traits of these new species, with respect to carbohydrate utilization, have also been determined. PMID:22230464

Thompson, J; Pikis, A

2011-10-04

358

Genetic relationships between Indians and their neighboring populations.  

PubMed

Using gene frequency data for 18 protein and blood group loci, we studied the genetic relationships of four Indian subcontinent populations (peoples from Punjab, Gujarati, Andhra Pradesh, and Bangladesh) with their neighboring populations (Iranians, Afghans, Sinhalese in Sri Lanka, Nepalese, Bhutanese, Malays, Bataks in northern Sumatra, and Chinese). The results obtained indicate that the four Indian subcontinent populations and the Sinhalese are genetically closer to Iranians and Afghans (Caucasoid) than to the other neighboring Mongoloid populations. Genetic distance analysis shows a clear-cut dichotomy between the Caucasoid and Mongoloid populations. PMID:4029959

Roychoudhury, A K; Nei, M

1985-01-01

359

Comparison of genetic diversity structure analyses of SSR molecular marker data within apple (Malus×domestica) genetic resources.  

PubMed

The aim of this study was to compare traditional hierarchical clustering techniques and principal coordinate analysis (PCoA) with the model-based Bayesian cluster analyses in relation to subpopulation differentiation based on breeding history and geographical origin of apple (Malus×domestica Borkh.) cultivars and landraces. We presented the use of a set of 10 microsatellite (SSR) loci for genetic diversity structure analyses of 273 apple accessions from national genetic resources. These SSR loci yielded a total of 113 polymorphic SSR alleles, with 5-18 alleles per locus. SSR molecular data were successfully used in binary and allelic input format for all genetic diversity analyses, but allelic molecular data did not reveal reliable results with the NTSYS-pc and BAPS softwares. A traditional cluster analysis still provided an easy and effective way for determining genetic diversity structure in the apple germplasm collection. A model-based Bayesian analysis also provided the clustering results in accordance to traditional cluster analysis, but the analyses were distorted by the presence of a dominant group of apple genetic resources owing to the narrow origin of the apple genome. PCoA confirmed that there were no noticeable differences in genetic diversity structure of apple genetic resources during the breeding history. The results of our analyses are useful in the context of enhancing apple collection management, sampling of core collections, and improving breeding processes. PMID:22954156

Patzak, Josef; Paprštein, František; Henychová, Alena; Sedlák, Ji?í

2012-09-06

360

Compromising genetic diversity in the wild: Unmonitored large-scale ...  

Treesearch

While adverse genetic impacts are recognized and documented in fisheries, little effort is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated with releases are largely ... Last Modified: July 21, 2013.

361

Impact of founder population, drift and selection on the genetic diversity of a recently translocated tree population  

Microsoft Academic Search

Recently established, temperate tree populations combine a high level of differentiation for adaptive traits, suggesting rapid genetic evolution, with a high level of genetic diversity within population, suggesting a limited impact of genetic drift and purifying selection. To study experimentally the evolutionary forces in a recently established population, we assessed the spatial and temporal patterns of genetic diversity within a

F Lefèvre; B Fady; D Fallour-Rubio; D Ghosn; M Bariteau

2004-01-01

362

WEED INVASION AND DIVERSITY RELATIONSHIPS IN PASTURE COMMUNITIES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Ecological research has shown that high plant diversity can reduce weed invasion in some plant communities. In 1999, we began a study to determine whether greater forage diversity in cool season pastures could reduce weed abundance. The study consisted of three components. First, weed abundance wa...

363

FORAGE DIVERSITY AND WEED ABUNDANCE RELATIONSHIPS IN GRAZED PASTURE COMMUNITIES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Studies have shown that weed invasion into grasslands may be suppressed in diverse plant communities. Our main objective was to determine whether increased forage plant diversity in pasture communities could help reduce weed abundance in the aboveground vegetation and soil seed bank. We also teste...

364

Genetic Education to Diverse Communities Employing a Community Empowerment Model  

Microsoft Academic Search

Lack of equity in access to health care, in general, and genetic services in particular, places communities of color at a distinct disadvantage when considering the rapidly evolving genetic technology. Much of this disparity is owed to lack of trust and credibility in the genetic care system as well as multiple ethnocultural barriers to services. This paper presents a 3-year

Ilana Suez Mittman

1998-01-01

365

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

2013-01-10

366

Genetic diversity through the looking glass: Effect of enrichment bias  

Microsoft Academic Search

The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D{sup +}) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations

JOHN DUNBAR; L. Forney; S. White

1997-01-01

367

Genetic relationships among 527 Gram-negative bacterial plasmids.  

PubMed

Plasmids are mosaic in composition with a maintenance "backbone" as well as "accessory" genes obtained via horizontal gene transfer. This horizontal gene transfer complicates the study of their genetic relationships. We describe a method for relating a large number of Gram-negative (GN) bacterial plasmids based on their genetic sequences. Complete coding gene sequences of 527 GN bacterial plasmids were obtained from NCBI. Initial classification of their genetic relationships was accomplished using a computational approach analogous to hybridization of "mixed-genome microarrays." Because of this similarity, the phrase "virtual hybridization" is used to describe this approach. Protein sequences generated from the gene sequences were randomly chosen to serve as "probes" for the virtual arrays, and virtual hybridization for each GN plasmid was achieved using BLASTp. Each resulting intensity matrix was used to generate a distance matrix from which an initial tree was constructed. Relationships were refined for several clusters by identifying conserved proteins within a cluster. Multiple-sequence alignment was applied to the concatenated conserved proteins, and maximum likelihood was used to generate relationships from the results of the alignment. While it is not possible to prove that the genetic relationships among the 527 GN bacterial plasmids obtained in this study are correct, replication of identical results produced in a separate study for a small group of IncA/C plasmids provides evidence that the approach used can correctly predict genetic relationships. In addition, results obtained for clusters of Borrelia plasmids are consistent with the expected exclusivity for plasmids from this genus. Finally, the 527-plasmid tree was used to study the distribution of four common antibiotic resistance genes. PMID:22587825

Zhou, Yunyun; Call, Douglas R; Broschat, Shira L

2012-05-12

368

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.

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

369

Tetraploid wheat landraces in the Mediterranean basin: taxonomy, evolution and genetic diversity.  

PubMed

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

2012-05-16

370

GENETIC DIVERSITY FOR LIPID CONTENT AND FATTY ACID PROFILE IN RICE BRAN  

Technology Transfer Automated Retrieval System (TEKTRAN)

Rice bran contains valuable nutritional constituents, which include lipids. A germplasm collection consisting of 204 genetically diverse rice accessions was grown under field conditions and evaluated for total oil content and fatty acid composition. Genotype effects were highly statistically signifi...

371

Compare Identity By Sequence Relationships of the Ames Diversity Panel using TYPSimSelector [abstract  

Technology Transfer Automated Retrieval System (TEKTRAN)

Maize genetic diversity has been exploited by mankind for 10,000 years. Scientific approaches applied to it by breeders for over a century transformed it into the world’s number one crop. Maize genomic diversity provides a rich resource of interest to evolutionary and population geneticists, constit...

372

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia  

PubMed Central

Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

2010-01-01

373

Genetic diversity and population structure of the invasive alien red swamp crayfish  

Microsoft Academic Search

High genetic diversity is thought to characterize successful invasive species, as the potential to adapt to new environments\\u000a is enhanced and inbreeding is reduced. The red swamp crayfish, Procambarus clarkii, native to northeastern Mexico and south-central USA was introduced to Nanjing, China from Japan in 1929. Little is known\\u000a about the genetic diversity and population structure of this species in

Gen Hua Yue; Jiale Li; Zhiyi Bai; Chun Ming Wang; Felicia Feng

2010-01-01

374

Spatio-temporal dynamics of genetic diversity in Sorghum bicolor in Niger  

Microsoft Academic Search

The dynamics of crop genetic diversity need to be assessed to draw up monitoring and conservation priorities. However, few\\u000a surveys have been conducted in centres of diversity. Sub-Saharan Africa is the centre of origin of sorghum. Most Sahel countries\\u000a have been faced with major human, environmental and social changes in recent decades, which are suspected to cause genetic\\u000a erosion. Sorghum

Monique Deu; F. Sagnard; J. Chantereau; C. Calatayud; Y. Vigouroux; J. L. Pham; C. Mariac; I. Kapran; A. Mamadou; B. Gérard; J. Ndjeunga; G. Bezançon

2010-01-01

375

Genetic erosion of sorghum ( Sorghum bicolor (L.) Moench) in the centre of diversity, Ethiopia  

Microsoft Academic Search

The Ethiopian region is characterised by a wide range of agro-climatic conditions, which accounted for the enormous resources\\u000a of agro-biodiversity that exist in the country. The most important of these resources is the immense genetic diversity of\\u000a the various crop plants in the country. Of these, one of the most on farm genetically diverse crops is sorghum. Since the\\u000a advent

Firew Mekbib

2008-01-01

376

Traditional knowledge and genetic diversity of opuntia pilifera (cactaceae) in the tehuacán-cuicatlán valley, Mexico  

Microsoft Academic Search

Traditional Knowledge and Genetic Diversity of Opuntia pilifera (Cactaceae) in the Tehuacán-Cuicatlán Valley, Mexico. Economic Botany 59(4)366-376, 2005. Most studies of the genusOpuntia have focused on economically important species, and therefore more knowledge concerning the genetic diversity among wild\\u000a and locally managedOpuntia species is needed for an expanded use of cacti in the future. The present study is part of

Linn Borgen Nilsen; Manfred Heun; Shivcharn S. Dhillion; Camargo-Ricalde Sara LucÍa; Rendón-Aguilar Beatriz

2005-01-01

377

Genetic diversity of Darnel ( Lolium temulentum L.) in Malo, Ethiopia depends on traditional farming systems  

Microsoft Academic Search

Genetic Diversity of Darnel (Lolium temulentum L.) in Malo, Ethiopia Depends on Traditional Farming Systems. Economic Botany 58(4):568–577, 2004. Darnel (Lolium temulentum L.) is a mimic weed associated with wheat and barley cultivation. Mimic weeds have evolved along with cultivated crops. Human\\u000a impact on the genetic diversity of agricultural weeds was elucidated using darnel as a model. Three strains in

Takayuki Senda; Tohru Tominaga

2004-01-01

378

Genetic Diversity of Cheju Horses ( Equus caballus ) Determined by Using Mitochondrial DNA D-loop Polymorphism  

Microsoft Academic Search

We used sequence polymorphism of the mitochondrial DNA D-loop (968 bp excluding the tandem repeat region) to determine genetic diversity of horses inhabiting Cheju (a southern island of Korea). Seventeen haplotypes with frequencies from 1.5 to 21.5% were found among 65 Cheju horse samples. Genetic diversity (h) of the 17 haplotypes was calculated to be 0.91, indicating that the extant

Y. H. Yang; K. I. Kim; E. G. Cothran; A. R. Flannery

2002-01-01

379

Genetic diversity and structure of blue pine ( Pinus wallichiana Jackson) in Bhutan  

Microsoft Academic Search

Blue pine (Pinuswallichiana Jackson) is a member of subsection Strobi that is an important component of middle- and high-elevation Himalayan forests. Five natural populations of P. wallichiana in Bhutan were investigated by starch–gel electrophoresis in an effort to determine the extent and distribution of genetic diversity. The level of genetic diversity was relatively high (A=1.8; P95=54.0%; Ho=0.163; He=0.168) and the

S. W Lee; W. Y Choi; L Norbu; R Pradhan

1998-01-01

380

Low genetic diversity among Cucumber vein yellowing virus isolates from Spain  

Microsoft Academic Search

The population structure and genetic diversity of Cucumber vein yellowing virus (CVYV) from Spain were estimated by analyses of partial nucleotide sequences of the P1-proteinase (P1-Pro), P3 protein (P3),\\u000a and the coat protein (CP) coding regions. Analysis of 56 CVYV Spanish field isolates collected from 2001 to 2005 showed low\\u000a genetic diversity (0.0026, 0.0013, and 0.0012 for the P1-Pro, P3,

Dirk Janssen; Leonardo Velasco; Germán Martín; Eduardo Segundo; Isabel Maria Cuadrado

2007-01-01

381

Genetic diversity of wild coffee ( Coffea arabica L.) using molecular markers  

Microsoft Academic Search

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre\\u000a of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica\\u000a and Bourbon, spread in the 18th century, which gave rise to the most currently grown

F. Anthony; B. Bertrand; O. Quiros; A. Wilches; P. Lashermes; J. Berthaud; A. Charrier

2001-01-01

382

Genetic diversity and structure of natural and transplanted eelgrass populations in the Chesapeake and Chincoteague Bays  

Microsoft Academic Search

The objective of this study was to gain baseline population data on the genetic diversity and differentiation of eelgrass\\u000a (Zostera marïna L.) populations in the Chesapeake and Chincoteague bays. Natural and transplanted eelgrass beds were compared using starch\\u000a gel electrophoresis of allozymes. Transplanted eelgrass beds were not reduced in genetic diversity compared with natural beds.\\u000a Inbreeding coefficients (FIS) indicated that

Susan L. Williams; Robert J. Orth

1998-01-01

383

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

384

Genetic Diversity of a Parasitic Weed, Striga hermonthica , on Sorghum and Pearl Millet in Mali  

Microsoft Academic Search

Eleven populations of witchweed, Striga hermonthica, were collected in four regions of Mali and investigated with 12 microsatellite markers. Extensive genetic diversity was\\u000a observed, with most plants heterozygous for most markers. Allelic diversity was broadly distributed across populations with\\u000a little genetic differentiation and large amounts of gene flow. Nearby fields of pearl millet and sorghum were found to have\\u000a indistinguishable

Matt C. Estep; Thomas A. Van Mourik; Peter Muth; Diarah Guindo; Heiko K. Parzies; Ousmane A. Koita; Eva Weltzien; Jeffrey L. Bennetzen

2011-01-01

385

Multilocus Sequence Typing for Studying Genetic Relationships among Yersinia Species  

PubMed Central

The intra- and interspecies genetic relationships of 58 strains representing all currently known species of the genus Yersinia were examined by multilocus sequence typing (MLST), using sequence data from 16S RNA, glnA, gyrB, recA, and Y-HSP60 loci. Yersinia aldovae, Y. bercovieri, Y. intermedia, Y. pestis, Y. pseudotuberculosis, Y. rohdei, and Y. ruckeri were genetically more homogeneous than were Y. enterocolitica, Y. frederiksenii, Y. kristensenii, and Y. mollaretii. The MLST data concerning the genetic relatedness within and among various species of Yersinia support the idea that Y. pestis and Y. pseudotuberculosis are two lineages within the same species rather than two distinct species. Y. ruckeri is the genetically most distant species within the genus. There was evidence of O-antigen switching and genetic recombination within and among various species of Yersinia. The genetic relatedness data obtained by MLST of the four housekeeping genes and 16S RNA agreed in most, but not all, instances. MLST was better suited for determining genetic relatedness among yersiniae than was 16S RNA analysis. Some strains of Y. frederiksenii and Y. kristensenii are genetically less related to other strains within those species, compared to strains of all other species within the genus. The taxonomic standing of these strains should be further examined because they may represent currently unrecognized Yersinia species.

Kotetishvili, Mamuka; Kreger, Arnold; Wauters, Georges; Morris, J. Glenn; Sulakvelidze, Alexander; Stine, O. Colin

2005-01-01

386

Genetic diversity of Annona crassiflora (Annonaceae) in northern Minas Gerais State.  

PubMed

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

Cota, L G; Vieira, F A; Melo Júnior, A F; Brandão, M M; Santana, K N O; Guedes, M L; Oliveira, D A

2011-09-23

387

Genetic relationship between Kangal, Akbash and other dog populations  

Microsoft Academic Search

Kangal and Akbash dogs are the two well-known shepherd dog breeds in Turkey. In order to contribute to the understanding of the genetic relationship between Kangal dogs, Akbash dogs and the dogs from different regions of Eurasia, 585 base pair (bp) segment of mitochondrial DNA (mtDNA) control region was sequenced from Kangals and Akbashes. Sequences of the Kangal and Akbash

Evren Koban; Çigdem Gökçek Saraç; Sinan Can Açan; Peter Savolainen; Inci Togan

2009-01-01

388

GENETIC RELATIONSHIPS AMONG FERTILITY TRAITS OF HOLSTEINS AND JERSEYS  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

389

Genetic relationship of meat and milk production in Finnish Ayrshire  

Microsoft Academic Search

Genetic relationships of meat and milk production traits were studied from a field data set of 50?852 Finnish Ayrshire bulls and heifers and 28?362 Finnish Ayrshire cows, using REML methodology and animal model. Studied meat production traits included carcass weight, fatness and fleshiness for all bulls, heifers and cows, and additionally heifer and mature live weights estimated based on heart

Anna-Elisa Liinamo; Matti Ojala; Johan van Arendonk

2001-01-01

390

Subspecific relationships and genetic structure in the spotted owl  

Microsoft Academic Search

Hierarchical genetic structure was examined in the three geographically-defined subspecies of spotted owl (Strix occidentalis) to define relationships among subspecies and quantify variation within and among regional and local populations. Sequences (522 bp) from domains I and II of the mitochondrial control region were analyzed for 213 individuals from 30 local breeding areas. Results confirmed significant differences between northern spotted

Susan M. Haig; Thomas D. Mullins; Eric D. Forsman

2004-01-01

391

Genetic diversity in three endangered pitcher plant species (Sarracenia; Sarraceniaceae) is lower than widespread congeners.  

PubMed

• Premise of the study: Narrow-ranging, rare species often exhibit levels of genetic diversity lower than more common or widespread congeners. These taxa are at increased risk of extinction due to threats associated with natural as well as anthropogenic events. We assessed genetic variation in three federally endangered Sarracenia species. We discuss maintenance of genetic diversity and evolutionary implications of rarity. • Methods: We analyzed three noncoding chloroplast regions and nine microsatellite loci in populations spanning the geographic ranges of S. oreophila, S. alabamensis, and S. jonesii. The same microsatellite loci were used to examine a single field site of three more widespread species (S. alata, S. leucophylla, and S. rubra subsp. wherryi). • Key results: All three endangered species have experienced reductions in population size and numbers. All show considerably less variation than more widespread members of the genus. Sarracenia alabamensis maintains the greatest microsatellite variation but has the fewest remaining populations and may be under the greatest threat. More widespread S. oreophila maintains surprising chloroplast diversity, yet exhibits little microsatellite diversity. Sarracenia jonesii lacks chloroplast diversity, yet maintains greater microsatellite diversity than S. oreophila. • Conclusions: The three endangered species differ in levels and structure of diversity, yet not in predictable ways, emphasizing that unique demographic and ecological histories, rather than current distribution and population size, best explain present patterns of genetic variation. Maintenance of remaining genetic variation is important, but preventing further habitat loss and degradation is critical. PMID:24088341

Furches, M Steven; Small, Randall L; Furches, Anna

2013-10-02

392

Genetic diversity and structure of Neotyphodium species and their host Achnatherum sibiricum in a natural grass-endophyte system.  

PubMed

Achnatherum sibiricum (Poaceae) is a perennial bunchgrass native to the Inner Mongolia Steppe of China. This grass is commonly infected by epichloë endophytes with high-infection frequencies. Previously, we identified two predominant Neotyphodium spp., N. sibiricum and N. gansuense. In the present study, genetic diversity and structure were analyzed for the two predominant Neotyphodium spp. as well as the host grass. We obtained 103 fungal isolates from five populations; 33 were identified as N. sibiricum and 61 as N. gansuense. All populations hosted both endophytic species, but genetic variation was much higher for N. gansuense than for N. sibiricum. The majority of fungal isolates were haploid, and 13% of them were heterozygous at one SSR locus, suggesting hybrid origins of those isolates. Significant linkage disequilibrium of fungal SSR loci suggested that both fungal species primarily propagate by clonal growth through plant seeds, whereas variation in genetic diversity and the presence of hybrids in both endophytic species revealed that although clonal propagation was prevalent, occasional recombination might also occur. By comparing genetic differentiation among populations, we found around 4-7-fold greater differentiation of endophyte populations than host populations, implying more restricted gene flow of endophytes than hosts. We proposed that endophyte infection of A. sibiricum might confer the host some selective advantages under certain conditions, which could help to maintain high-endophyte-infection frequencies in host populations, even when their gene flows do not match each other. Furthermore, we suggested that the same genotype of endophyte as well as host should be confirmed if the objective of the study is to know the influence of endophyte or host genotype on their symbiotic relationship, instead of just considering whether the plant is infected by an endophyte or not, since endophytes from the same host species could exhibit high levels of genetic diversity, which is likely to influence the outcome of their symbiotic relationship. PMID:20352205

Zhang, Xin; Ren, Anzhi; Ci, Huacong; Gao, Yubao

2010-03-30

393

A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains  

Microsoft Academic Search

Helicobacter pylori colonizes the stomach of half of the world's population, causing a wide spectrum of disease ranging from asymptomatic gastritis to ulcers to gastric cancer. Although the basis for these diverse clinical outcomes is not understood, more severe disease is associated with strains harboring a pathogenicity island. To characterize the genetic diversity of more and less virulent strains, we

Nina Salama; Karen Guillemin; Timothy K. McDaniel; Gavin Sherlock; Lucy Tompkins; Stanley Falkow

2000-01-01

394

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

395

Assessment of Genetic Diversity in Feronia limonia (L.) Swingle Using Inter Simple Sequence Repeats  

Microsoft Academic Search

Genetic variation was studied in threatened natural populations of Feronia limonia (Rutaceae). Samples were collected from 3 populations located in the Aravalli mountain range of south-east Rajasthan, India. Using 25 Inter Simple Sequence Repeat (ISSR) primer combinations, significant diversity was characterized among the individuals. Analysis of Molecular Variance (AMOVA) revealed that diversity is partitioned mainly within population components (80%). F

Shailendra Vyas; Anupama Gaur; Akhilesh K. Tyagi; Sunil Dutta Purohit

2008-01-01

396

GENETIC DIVERSITY IN POPULATIONS OF XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS IN CRUCIFEROUS WEEDS IN CENTRAL COASTAL CALIFORNIA  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

397

The Relationship between Diverse Components of Intelligence and Creativity  

ERIC Educational Resources Information Center

|Intelligence and creativity are accounted for in terms of two different mental operations referred to as "convergent thinking" and "divergent thinking", respectively. Nevertheless, psychometric evidence on the relationship between intelligence and creativity has been controversial. To clarify their relationship, we characterized the relationship

Cho, Sun Hee; Nijenhuis, Jan Te; van Vianen, Annelies E. M.; Kim, Heui Baik; Lee, Kun Ho

2010-01-01

398

Allozyme diversity and genetic structure of the leafy cactus (Pereskia guamacho [Cactaceae]).  

PubMed

We examined levels of genetic variation and genetic structure in the leafy cactus (Pereskia guamacho) in arid and semiarid zones in Venezuela. We surveyed genetic diversity within 17 populations using 19 allozyme loci. Genetic diversity was relatively high at both the species (P(s) = 89%, A(s) = 3.26, AP(s) = 3.53, H(es) = 0.24) and population (P(p) = 63%, A(p) = 1.90, AP(p) = 2.42, H(ep) = 0.20) levels. A significant deficit of heterozygote individuals was detected within populations in the Paraguana Peninsula region (F(IS) = 0.301). Relatively low levels of population differentiation were detected at macrogeographic (G(ST) = 0.112) and regional levels (G(ST) = 0.044 for peninsula region and G(ST) = 0.074 for mainland region), suggesting substantial genetic exchange among populations; however, gene flow in this species seems to be regulated by the distance among populations. Overall, estimates of genetic diversity found in P. guamacho are concordant with the pattern observed for other cacti surveyed, namely high levels of polymorphism and genetic diversity with one common allele and several rare alleles per locus. Differences in gene dispersal systems between this species and other cacti studied were not reflected in the patterns of genetic diversity observed. The concentration of the highest estimates of genetic variation in northwestern Venezuela suggests a potential reservoir of plant genetic diversity within xerophilous ecosystems in northern South America. PMID:12195035

Nassar, J M; Hamrick, J L; Fleming, T H

399

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

2012-12-06

400

Genetic diversity of Mexican brook lamprey Lampetra (Tetrapleurodon) geminis (Alvarez del Villar, 1966).  

PubMed

Lampreys are the only surviving representatives of the oldest known vertebrates. The Mexican lamprey L. geminis (nonparasitic), is particularly interesting, because it is an endemic, biogeographical relict, and a threatened species. RAPD markers were used to describe genetic diversity in L. geminis. A total of 77 specimens were collected from five populations, three in the Río Grande de Morelia-Cuitzeo basin and two in the Río Duero-Lerma-Chapala basin, México. Eighty-eight RAPD markers were obtained from eight primers. Genetic diversity within each population was estimated using Shannon's index (S), heterozygosity (H) and gene diversity (h). These estimates revealed significant variation within populations, although a variance homogeneity test (HOMOVA) showed no significant differences among populations or between basins. Nei genetic distance values indicate a low genetic differentiation among populations. Analysis of molecular variance (AMOVA) indicates that most of the genetic diversity occurs within populations (91.4%), but that a statistically significant amount is found among populations (P < 0.001). Principal coordinates and cluster analyses of RAPD phenotypes show that specimens are not grouped by geographical origin. The genetic diversity found within L. geminis populations may be explained by its breeding system and an overlapping of generations. The scarce genetic differentiation among populations is likely to the low rate of DNA change that characterizes the lamprey group. PMID:15609555

Mejía, Omar; Polaco, Oscar J; Zúñiga, Gerardo

2004-11-01

401

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.

Porlier, Melody; Belisle, Marc; Garant, Dany

2009-01-01

402

Colonization processes and the maintenance of genetic diversity: insights from a pioneer rainforest tree, Aucoumea klaineana  

PubMed Central

Despite recurrent episodes of range expansion and contraction, forest trees often harbour high genetic diversity. Studies of temperate forest trees suggest that prolonged juvenile phase and high pollen flow are the main factors limiting founder effects. Here, we studied the local colonization process of a pioneer rainforest tree in central Africa, Aucoumea klaineana. We identified 87% of parents among trees up to 20–25 years old and could thus compare direct parentage structure data with classical population genetics estimators. In this species, genetic diversity was maintained during colonization. The absence of founder effects was explained by (i) local random mating and (ii) local recruitment, as we showed that 75% of the trees in the close neighbourhood participated in the recruitment of new saplings. Long-distance pollen flow contributed little to genetic diversity: pollen and seed dispersal was mainly within stand (128 and 118 m, respectively). Spatial genetic structure was explained by aggregated seed dispersal rather than by mother–offspring proximity as assumed in classical isolation-by-distance models. Hence, A. klaineana presents a genetic diversity pattern typical of forest trees but does not follow the classical rules by which this diversity is generally achieved. We suggest that while high local genetic variability is of general importance to forest tree survival, the proximate mechanisms by which it is achieved may follow very different scenarios.

Born, Celine; Kjellberg, Finn; Chevallier, Marie-Helene; Vignes, Helene; Dikangadissi, Jean-Toussaint; Sanguie, Jodel; Wickings, E. Jean; Hossaert-McKey, Martine

2008-01-01

403

Assessing genetic diversity of cotton cultivars using genomic and newly developed expressed sequence tag-derived microsatellite markers.  

PubMed

Estimations of genetic diversity and of relationships between varieties are crucial for cotton breeding. The genetic diversity of 59 core cotton cultivars, most of which were collected from China's main cotton-growing areas, was analyzed based on genomic and newly developed expressed sequence tag-derived microsatellite markers, using total DNA extracted from fresh leaf tissue. Three hundred and two fragments were detected, of which 255 were polymorphic. The number of amplification products generated by each primer varied from 2 to 14, with a mean of 5.08 bands/primer. The polymorphism information content was 0.50 to 0.90, with a mean of 0.80. The genetic similarity coefficients were calculated and dendrograms were constructed by the unweighted pair group with arithmetic mean method; the resulting distance matrix gave a dendrogram with four main clusters. Some cultivars with similar pedigrees could be clustered. For example, Zhong206 and Shanmian4, both derived from Deltapine15, were clustered. The genetic similarity coefficient of the 59 core cultivars ranged from 0.53 to 0.99, with a mean of 0.72, indicating that there was a relatively high level of genetic variation. PMID:21823096

Zhang, Y; Wang, X F; Li, Z K; Zhang, G Y; Ma, Z Y

2011-01-01

404

An AFLP-based survey of genetic diversity among accessions of sea oats (Uniola paniculata, Poaceae) from the southeastern Atlantic and Gulf coast states of the United States.  

PubMed

Uniola paniculata, commonly known as sea oats, is a C4 perennial grass capable of stabilizing sand dunes. It is most abundant along the Gulf of Mexico and southeastern Atlantic coastal regions of the United States. The species exhibits low seed set and low rates of germination and seedling emergence, and so extensive clonal reproduction is achieved through production of rhizomes, which may contribute to a decline in genetic diversity. To date, there has been no systematic assessment of genetic variability and population structure in naturally occurring stands in the USA. This study was conducted to assess the genetic relationship and diversity among nineteen U. paniculata accessions representing eight states: Texas, Louisiana, Mississippi, Alabama, Florida, South Carolina, North Carolina, and Virginia, using amplified fragment length polymorphism (AFLP). Twelve AFLP EcoRI + MseI primer combinations generated a wide range of polymorphisms (42-81%) with a mean of 59%. Overall, the sea oats plants exhibited a low range of genetic similarity. Florida accessions, FL-33 and FL-39, were most genetically diverse and the accessions from both Carolinas and Virginia (NC-1, NC-11, SC-15, and VA-53) harbored less genetic variability. Cluster analysis using the UPGMA approach separated U. paniculata plants into four major clusters which were also confirmed by principal coordinate analysis (PCO). Further examination of the different components of genetic variation by analysis of molecular variance (AMOVA) indicated the largest proportion of variability at the state level (47.8%) followed by the variation due to the differences among the genotypes within an accession (34.4%), and the differences among the accessions within a state (17.8%). The relationship between genetic diversity and geographic source of sea oats populations of the United States as revealed through this comprehensive study will be helpful to resource managers and commercial nurseries in identifying suitable plant materials for restoration of new areas without compromising the adaptation and genetic diversity. PMID:16195884

Subudhi, Prasanta K; Parami, Neil P; Harrison, Stephen A; Materne, Michael D; Murphy, J Paul; Nash, David

2005-09-30

405

Effects of a recent founding event and intrinsic population dynamics on genetic diversity in an ungulate population  

Microsoft Academic Search

Maintenance of genetic diversity has recently become a management goal for a number of species, due to its importance for\\u000a present and future population viability. Genetic drift, primarily through differential reproductive success and inbreeding,\\u000a can accelerate the loss of genetic diversity in recently recovered populations. We attempt to quantify the consequences of\\u000a these factors on the genetic diversity contained in

Gregory A. Wilson; John S. Nishi; Brett T. Elkin; Curtis Strobeck

2005-01-01

406

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