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 ...
Artemisia halodendron (Asteraceae) is a dominant sand-fixing semi-shrub species native to the Horqin Sandy Land of northeastern China. In this study, we evaluated levels of genetic variation within and among sampled A. halodendron populations from two different hydrothermal regions of the Horqin Sandy Land using inter-simple sequence repeat (ISSR) markers. We also investigated possible relationships between genetic diversity of this species and climatic factors. Our analysis revealed that A. halodendron is highly genetically diverse, with populations from a low hydrothermal level region having higher genetic diversity index values than those from a high hydrothermal level region. An analysis of molecular variation (AMOVA) revealed relatively high levels (>89.83%) of within-population genetic variation. Based on cluster analysis, the 13 studied A. halodendron populations can be clustered into two clades. Genetic diversities of all populations have been influenced by many climatic factors, and Nei's genetic diversity (h) is strongly correlated with annual temperature range (ART). These results have important implications for restoration and management of degraded ecosystems in arid and semi-arid areas.
Huang, Wenda; Zhao, Xueyong; Zhao, Xin; Li, Yuqiang; Lian, Jie; Yun, Jianying
Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German
Eveline Mengwi Ibeagha-Awemu; Oliver Carl Jann; Christina Weimann; Georg Erhardt
Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit. PMID:22204023
Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert
Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups--African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided. PMID:15496287
Ibeagha-Awemu, Eveline Mengwi; Jann, Oliver Carl; Weimann, Christina; Erhardt, Georg
Population genetic theory predicts that long-term isolation of "living fossils" in relic habitats might reduce genetic variability due to small population sizes and inbreeding. The recent description of a troglodytic "living fossil" Congeria kusceri--the only known subterranean bivalve mollusc--from a genus thought to be extinct since the Miocene, offers a unique opportunity to examine this hypothesis. Here, we use DNA sequences from two mitochondrial genes to compare levels of genetic variability and to test phylogenetic relationships of C. kusceri with surface-dwelling dreissenid relatives. Phylogenetic analyses of sequences from the cytochrome oxidase 1 (COI) and 16S rDNA genes reveal that Mytilopsis is the sister genus to Congeria and this clade forms the sister taxon to Dreissena. Relatively high levels of DNA diversity characterized the population of C. kusceri (haplotypic diversity= 0.50 for 16S rDNA and 0.66 in the COI gene), in contrast to no intraspecific variability in populations of Dreissenapolymorpha, D. bugensis, Mytilopsisleucophaeta, and Corbiculafluminea. Maintenance of genetic variability in C. kusceri may result from long-term population size stability, which merits further investigation. This underground species apparently was buffered from the climatic changes and resultant population bottlenecks that affected its surface-dwelling relatives during the Pliocene and Pleistocene Ice Ages. PMID:11555232
Stepien, C A; Morton, B; Dabrowska, K A; Guarnera, R A; Radja, T; Radja, B
Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%), with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid) species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.
Awasthi, Arvind K; Nagaraja, GM; Naik, GV; Kanginakudru, Sriramana; Thangavelu, K; Nagaraju, Javaregowda
There has been a renewed interest in the effects of genetic diversity on population-level and community-level processes. Many of these studies have found non-additive, positive effects of diversity, but these studies have rarely examined ecological mechanisms by which diverse populations increase productivity. We used the seed beetle Callosobruchus maculatus (Coleoptera: Chrysomelidae) to study genetic diversity in insect host preference and fecundity and its effects on total productivity and resource use. We created genetically distinct lineages that varied in host preference and fecundity and then assembled groups consisting of one, three, five, or all ten lineages. We found that lineages with intermediate diversity had the highest productivity, though resource use did not change in diverse groups. In addition, lineages showed substantial plasticity in host preference when preference was assayed either individually or in groups, and productivity was much lower in groups than predicted by individual assays. These results highlight the interplay of genetic diversity, resource variation, and phenotypic plasticity in determining the ecological consequences of genetic diversity. In addition, when plasticity modifies a population's response to population density, this may create a complex interaction between genetic diversity and density, influencing selective pressures on the population and potentially maintaining genetic diversity across generations. PMID:24535057
Burls, K J; Shapiro, J; Forister, M L; Hoelzer, G A
Agropyron Gaertn. is the most important genus in Triticeae (Poaceae), which includes many forage grasses with high economic value. The genetic diversity and relationships of 36 accessions from five crested wheatgrass species were analyzed by gliadin markers. A total of 54 product bands were detected after acid polyacrylamide gel electrophoresis (A-PAGE), of which 100% were polymorphic. The genetic similarity coefficient based on Nei-Li's method ranged from 0.065 to 0.755 with an average of 0.451. The Shannon diversity information index showed that there was a high level of genetic diversity among the accessions. An unweighted pair group method with arithmetic average (UPGMA) dendrogram was constructed based on the Nei-Li's genetic similarity coefficients, which showed the phylogenetic relationships among accessions of different species. Analysis of molecular variance (AMOVA) showed that the proportion of variance explained by inter- and intraspecific variance was 9.34 and 90.66%, respectively, which revealed that the genetic variations within species were higher than the variations among species. Based on pairwise genetic distances (?ST) among species, the cluster analysis indicated that A. mongolicum had a low-affinity relationship with other species, while A. fragile showed a close relationship with A. cristatum ssp pectinatum. Finally, the implications of the results for the taxonomy of Agropyron were discussed. PMID:24301939
Chen, S Y; Ma, X; Zhang, X Q; Huang, L K; Zhou, J N
Diversity among 17 melon landraces and inbred lines of Group Cantalupensis, Inodorus, and Flexuosus germplasm from Greece\\u000a was assessed using 24 RAPD primers, 11 morphological traits of fruit, two yield-related characteristics, and resistance to\\u000a powdery mildew. Accessions were genetically diverse and the greatest variation was detected in Group Flexuosus. Comparative\\u000a analysis of Greek germplasm and an array of previously characterized
Jack E. Staub; Ana I. López-Sesé; Nikolaos Fanourakis
Background Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP). Results Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied. Conclusion We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.
Laurentin, Hernan E; Karlovsky, Petr
The genus Rhinanthus L. is complex, containing many taxonomically unresolved taxa. In this paper we studied genetic variation and species relationships in 15 populations of six Rhinanthus species from three sections. For this purpose, we developed new microsatellite primers for R. osiliensis and used them to investigate genetic variation in two narrow endemics (R. osiliensis, R. javorkae) and in four widespread species (R. rumelicus R. wagneri, R. angustifolius and R. minor). Species-specific private alleles were found in all species except R. osiliensis and R. angustifolius. The Bulgarian endemic R. javorkae showed the lowest genetic variation, followed by widespread R. minor and Estonian endemic R. osiliensis. Rhinanthus javorkae and R. minor were genetically most differentiated. Section Cleistolemus is weakly structured genetically, indicating close affinity between R. osiliensis, R. rumelicus, R. wagneri and R. angustifolius. PMID:23889942
Talve, T; McGlaughlin, M E; Helenurm, K; Wallace, L E; Oja, T
Elymus trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The phylogenetic\\u000a relationships among the E. trachycaulus complex, and their systematic relation to other species in Triticeae remain unknown. Nucleotide diversity of ribulose-1,5\\u000a bisphosphate-carboxylase (rbcL) gene in E. trachycaulus complex species and several other Triticeae was first characterized and compared. A primary
Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity\\u000a and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust\\u000a alternative, PCR based marker assays
Arvind K Awasthi; GM Nagaraja; GV Naik; Sriramana Kanginakudru; K Thangavelu; Javaregowda Nagaraju
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
Summary. Norovirus and Sapovirus are two genera of the family Caliciviridae that contain viruses that can cause acute gastroenteritis in humans. Noroviruses (NOR) are genetically highly diverse but limited studies of the genetic diversity of sapoviruses (SAP) have been reported. In this study we characterized twenty-five SAP detected in our laboratory from outbreaks or sporadic cases of acute gastroenteritis in
T. Farkas; W. M. Zhong; Y. Jing; P. W. Huang; S. M. Espinosa; N. Martinez; A. L. Morrow; G. M. Ruiz-Palacios; L. K. Pickering; X. Jiang
The study of relationships between cell size and productivity is of key importance in microbial ecology to understand which members of natural aquatic communities are responsible for the overall activity and/or productivity. Flow sorting of microorganisms from different environmental samples was used to analyze the activity of bacterial cells depending on their biovolume. Bacterial cells from five different natural samples taken along the Mediterranean coast including fresh- and seawaters were incubated with tritiated leucine, then stained with SYTO 13 and sorted by flow cytometry according to their average side-angle-scattered (SSC) light. In all samples, a bell-shaped relationship was found between cell biovolume and activity, whereas activity of a given cell-size class varied between samples. In contrast, an inverse relationship was found between biovolumes and abundances. These results suggest that medium-sized cells with highest growth rates are probably submitted to intense grazing. For one sample, bacteria within five different size classes were sorted and the genetic diversity of cells within each sorted size class and that of the whole community were analyzed by the denaturing gradient gel electrophoresis (DGGE) method. The genetic diversity, as determined at the community level was highly represented into the pool of small cells, whereas only few species were present into larger cell subpopulations. The results suggest that only a few genotypes may be dominant within the largest and most productive cells. Furthermore, cell size polymorphism as well as heterogeneous cellular activities were found within some species. PMID:11029083
Bernard; Courties; Servais; Troussellier; Petit; Lebaron
Yunnan is situated in the Southwest China and encompasses regions having high biodiversity, including habitats for several ancestral species of domestic animals such as chicken. Domestic chickens in Yunnan were kept by peoples of varied ethnic and economic backgrounds living in highly varied geographic environments. To identify the genetic background of Yunnan domestic chickens and their relationships with Red Junglefowl, we applied 28 widely used microsatellite DNA markers to genotype 340 birds from 7 chicken breeds and Red Junglefowl indigenous to Yunnan. Among a total of 342 alleles identified, 121 (35.4%) were breed specific, with Red Junglefowl harboring most microsatellite alleles (23). High levels of heterozygosity were observed within populations indicated by a mean unbiased HE value of 0.663, which was higher than the reported for most populations elsewhere. The FIS value of domestic populations ranged from -0.098-0.005, indicating a lack of inbreeding among these populations. A high proportion of significant departures (89) from the 224 HWE tests for each locus in each population reflected an excess of heterozygosity and population substructure. Individual assignment tests, high FST values (0.1757-0.3015), and Nei's DA genetic distances (0.4232-0.6950) indicated clear differentiation among these populations. These observations, along with the close genetic distance between indigenous domestic populations and Red Junglefowl, were consistent with the primitive and ancestral state of Yunnan indigenous chickens. Protecting the unique variants of these indigenous poultry varieties from contamination with commercial breeds might provide values for improving modern agricultural livestock and breeding programs. Thus, the current study may benefit breeding management and conservation efforts. PMID:24841782
Huo, J L; Wu, G S; Chen, T; Huo, H L; Yuan, F; Liu, L X; Ge, C R; Miao, Y W
In total, 166 individuals from five indigenous Ethiopian cattle populations – Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) – were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ?0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ?0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (FST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.
Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk
Modern sugarcane cultivars are genetically vulnerable because the narrow gene pool from which they are derived originated from a few inter-specific hybrids between Saccharum officinarum and its wild relatives, including S. spontaneum . Efforts are being made to broaden the genetic base of cultivated sugarcane through wide crosses with S. spontaneum and other related species and genera. The objective of
J. A. Arro; J. C. Veremis; C. A. Kimbeng; C. Botanga
In the present study, 24 Y-chromosomal short tandem repeat (Y-STR) loci were analyzed in 115 unrelated Hui male individuals from Haiyuan county or Tongxin county, Ningxia Hui Autonomous Region, China, to evaluate the forensic application of the 24 STR loci and to analyze interpopulation differentiations by making comparisons between the Hui group data and previously published data of other 13 populations. A total of 115 different haplotypes were observed on these 24 Y-STR loci. The gene diversities ranged from 0.4049 (DYS437) to 0.9729 (DYS385a, b). The overall haplotype diversity was 1 at AGCU 24 Y-STR loci level, while the values were reduced to 0.999237, 0.996949, and 0.996644 at the Y-filer 17 loci, 11 Y-STR loci of extended haplotype and 9 Y-STR loci of minimal haplotype levels, respectively; whereas, haplotype diversity for additional 7 loci (not included in Y-filer 17 loci) was 0.995271. The pairwise FST , multidimensional scaling plot and neighbor-joining tree indicated the Hui group had the closest genetic relationship with Sala in the paternal lineage in the present study. In summary, the results in our study indicated the 24 Y-STRs had a high level of polymorphism in Hui group and hence could be a powerful tool for forensic application and population genetic study. PMID:24789806
Zhu, Bo-Feng; Zhang, Yu-Dang; Liu, Wen-Juan; Meng, Hao-Tian; Yuan, Guo-Lian; Lv, Zhe; Dong, Nan; Li, Qiong; Yang, Chun-Hua; Zhang, Yu-Hong; Hou, Yin-Ling; Qian, Li; Fan, Shuan-Liang; Xu, Peng
Anthropogenic stressors that reduce population size, alter migration corridors or modify mutational and selective forces on populations are expected to leave a lasting genetic footprint on the distribution of intraspecific genetic variation. Thus, the pattern of intraspecific gen...
Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations. PMID:24466640
Rocañín-Arjó, Ares; Rodríguez-Botigué, Laura; Esteban, Esther; Theves, Catherine; Evdokimova, Larissa E; Fedorova, Sardana A; Gibert, Morgane; Crubezy, Eric; Moral, Pedro
Genetic variation between samples of Oryza sativa from 19 localities in Bangladesh and Bhutan was assessed using two PCR-based molecular marker systems: RAPD (random amplification of polymorphic DNA) and ISSR-PCR (inter-simple sequence repeat polymerase chain reaction). Employing RAPD, a set of 14 decanucleotides of arbitrary sequence directed the amplification of 94 reproducible marker bands, 47 (50%) of which were polymorphic.
Beverley J. Parsons; H. John Newbury; Michael T. Jackson; Brian V. Ford-Lloyd
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\\u000a were analyzed. The 25 LCDV isolates examined in this study were attributed to seven LCDV genotypes: genotype I
Xiu-Ying Yan; Zao-He Wu; Ji-Chang Jian; Yi-Shan Lu; Xiu-qin Sun
Prunus microcarpa C.A. Mey. subsp. tortusa is a deciduous shrub well adapted to severe winter and dry-hot summer conditions. As the first step to explore the genetic and horticultural potential of P. microcarpa C.A. Mey. subsp. tortusa, we used SSRs to elucidate the genetic variation within its populations dispersed in upper Mesopotamia. We also investigated its phylogenetic relationship with economically
Mehmet Nuri Nas; Yuksel Bolek; Adem Bardak
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.
The population structuring and low genetic diversity of the Manchurian zokor Myospalax psilurus Milne-Edwards, 1874, an East Asian endemic included in the Red List of Russia, were demonstrated. Two separate geographical groups differing in the level of their genetic diversity were found on the territory of the Primorskii krai. The subpopulation located closest to the main area of this species was determined as ancestral. A subspecies differentiation of the Primorskii krai and Transbaikal M. psilurus populations was shown, as was the monophyletic origin of M. psilurus and its high divergence from M. aspalax. The animals from northern localities are recommended for reintroduction in nature under species recovery programs in Primorskii krai. PMID:21789993
Chelomina, G N; Korablev, V P; Pavlenko, M V
DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes. PMID:24783778
Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A
Based on our review of literature and survey of geneticists working on California taxa, we find genetic information lacking for most spe- cies in the Sierra Nevada. This situation is likely to remain in the future, with specific groups of taxa or occasional rare or high-interest species receiving specific study. Where we do have empirical infor- mation, we find few
DEBORAH L. ROGERS; CONSTANCE I. MILLAR; ROBERT D. WESTFALL
Chemical constituents and evolutionally neutral DNA sequences of six samples of Cremanthodium lineare Maxim., collected in the Sichuan Province of China, were studied. Three samples produced furanoeremophilanes and the other three, eremophilan-8-ones. The chemotypes were found to be correlated with DNA sequence types, suggesting that the chemical diversity observed has a genetic origin. Production of furanoeremophilanes by a Cremanthodium species suggests an evolutionary relationship between Cremanthodium and Ligularia species, and possibly to related genera. PMID:24119572
Saito, Yoshinori; Ichihara, Mayu; Takiguchi, Koji; Tanio, Yui; Okamoto, Yasuko; Hanai, Ryo; Kuroda, Chiaki; Kawahara, Takayuki; Gong, Xun; Tori, Motoo
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
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
A genetic diversity study of Koompassia malaccensis based on 19 populations from 18 forest reserves in Peninsular Malaysia is reported. The genetic diversity assessment was based on six polymorphic microsatellites. Overall, all the populations showed high levels of genetic diversity. The allelic richness ranged from 6.0 (Pekan) to 9.3 (Lenggor) whereas the gene diversity ranged from 0.683 (Pekan) to 0.859
C. T. Lee; S. L. Lee; Q. Z. Faridah; S. S. Siraj; K. K. S. Ng; M. Norwati
Mammals have evolved a variety of morphological adaptations that have allowed them to compete in their natural environments. The developmental genetic basis of this morphological diversity remains largely unknown. Bats are mammals that have the unique ability of powered flight. We have examined the molecular embryology of bats and investigated the developmental genetic basis for their highly derived limbs used for flight. Initially, we developed an embryo staging system for a model chiropteran, Carollia perspicillata, the short-tailed fruit bat that has subsequently been used for staging other bat species. Expression studies focusing on genes that regulate limb development indicate that there are similarities and differences between bats and mice. To determine the consequences of these expression differences, we have conducted an enhancer switch assay by gene targeting in mouse embryonic stem cells to create mice whose genes are regulated by bat sequences. Our studies indicate that cis-regulatory elements contribute to the morphological differences that have evolved among mammalian species.
Behringer, R.R.; Rasweiler, J.J.; Chen, C.-H.; Cretekos, C.J.
RAPD assays were performed, using 34 arbitrary decamer oligonucleotide primers and six combinations of two primers, to detect inherent variations and genetic relationships among 12 Indian and 11 exotic B. juncea genotypes. Of 595 amplification products identified, 500 of them were polymorphic across all genotypes. A low level of genetic variability was detected among the Indian genotypes, while considerable polymorphism
A. Jain; S. Bhatia; S. S. Banga; S. Prakash; M. Lakshmikumaran
Chromosomal diversity and relationships among 126 Streptococcus pyogenes strains expressing M1 protein from 13 countries on five continents were analyzed by multilocus enzyme electrophoresis and restriction fragment profiling by pulsed-field gel electrophoresis. All isolates were studied for the presence of the gene encoding streptococcal pyrogenic exotoxin A by PCR. Strain subsets were also examined by automated DNA sequencing for allelic polymorphism in genes encoding M protein (emm), streptococcal pyrogenic exotoxin A (speA), streptokinase (ska), pyrogenic exotoxin B (interleukin-1 beta convertase) (speB), and C5a peptidase (scp). Seven distinct emm1 alleles that encode M proteins differing at one or more amino acids in the N-terminal variable region were identified. Although substantial levels of genetic diversity exist among M1-expressing organisms, most invasive disease episodes are caused by two subclones marked by distinctive multilocus enzyme electrophoretic profiles and pulsed-field gel electrophoresis restriction fragment length polymorphism (RFLP) types. One of these subclones (ET 1/RFLP pattern 1a) has the speA gene and was recovered worldwide. Identity of speA, emm1, speB, and ska alleles in virtually all isolates of ET 1/RFLP type 1a means that these organisms share a common ancestor and that global dispersion of this M1-expressing subclone has occurred very recently. The occurrence of the same emm and ska alleles in strains that are well differentiated in overall chromosomal character demonstrates that horizontal transfer and recombination play a fundamental role in diversifying natural populations of S. pyogenes.
Musser, J M; Kapur, V; Szeto, J; Pan, X; Swanson, D S; Martin, D R
A taxonomic study was carried out for isolates of Saccharomyces spp. identified as contaminants ("wild yeast") in 24 different lager breweries. With reference to the current taxonomy all isolates were found to belong to the Saccharomyces sensu stricto complex and 58% of the isolates were further identified as S. cerevisiae, 26% as S. pastorianus and 3% as S. bayanus. The remaining isolates (13%) could not be identified to the species level based on their phenotypic characteristics. However, some of these isolates were identified as S. cerevisiae by HaeIII restriction digest of PCR-amplified intergenic transcribed spacer (ITS) regions. Chromosome length polymorphism (CLP) was evident among the Saccharomyces brewing contaminants with chromosome profiles typical of Saccharomyces sensu stricto. Based upon cluster analysis of their chromosome profiles the majority of the brewing contaminants could be grouped as either S. cerevisiae or S. pastorianus/S. bayanus. Further, the technique was able to differentiate between almost all brewing contaminants and to separate them from any specific lager brewing yeast. The diversity of the Saccharomyces brewing contaminants clearly demonstrated by their CLP was further reflected by MAL genotyping. For the majority of the isolates more than two MAL loci were found with MAL1, MAL2 MAL3, MAL4 and MAL11, MAL31, MAL41 as the dominant genotypes. For all isolates MAL11 and MAL31 were found whereas MAL61 only was found for one isolate. The high number of MAL loci found in the SaccharomYces brewing contaminants indicate their adaptation to a maltose-enriched environment. PMID:11014521
Jespersen, L; van der Kühle, A; Petersen, K M
To determine the genetic diversity of Haloxylon ammodendron collected from 14 sites in 5 provinces, 103 H. ammodendron samples of 12 wild populations and 2 cultivated which collected from 14 sites in 5 provinces were analyzed by amplified fragment length polymorphism (AFLP) DNA markers. PopGen32 and NTSYSpc2.1 was applied to evaluate genetic diversity of H. ammodendron populations. The average percentage of polymorphic loci (PPL) of total H. ammodendron populations was 94.13%, the average Nei's gene diversity index (H(e)) from 14 populations was 0.308 0, and the Shannon's genetic diversity index (I) was 0.467 6. The results indicated that the genetic diversity of H. ammodendron populations was high. Genetic differentiation index (G(st)) was 0.313 8, and the gene flow (N(m)) was 1.093 5 at the population level. The level of gene flow of H. ammodendron showed it possessed the feature of wind-pollinated outcrossing plants. AMOVA analysis indicated that genetic variation of H. ammodendron was much higher within groups (89.34%) than that among groups (10.66%), moreover genetic variation within groups mainly occurred among populations in different producing areas (84.80%). Cluster analysis (UPGMA) was applied to generate dendrogram based on Nei's genetic distances of 14 populations. Samples from Xinjiang and Qinghai were clustered respectively as a clade for their distant genetic relationship, while Samples from Gansu, Inner Mongolia and Ningxia were clustered together for their close genetic relationship. Genetic diversity of H. ammodendron populations is high in China, and genetic differentiation among regions is small, thus abundance within this specie is high at this stage. Therefore, wild nursery and artificial cultivating in different areas are effective measures for the conservation and sustainable utilization of H. ammodendron resources. PMID:24956833
Shen, Liang; Xu, Rong; Chen, Jun; Chen, An-Ping; Zhu, Guo-Qiang; Lv, Jia; Wang, Wei; Liu, Tong-Ning
B19 Parvovirus (B19V) has been considered for a long period of time as the unique human virus belonging to the genus Erythrovirus. The genetic diversity of B19V isolates has been shown to be very low (<2% nucleotide divergence). The isolation of a variant (V9 strain), with a sequence markedly distinct from that of B19V (>13% nucleotide divergence) led to specify the classification of this virus family. Phylogenetic analysis of partial sequences of V9-related isolates combined with Erythrovirus sequences in sequences banks indicates an organization into three well-individualized genotypes. Analysis of the nearly full-length genome sequences show an ancient separation between the three genotypes lineages. Genotype 3 (the most ancient lineage) could have originated in Africa. The functional regions of major proteins are conserved in the three genotypes. The frequency of these genotypes is various according to studies. Genotype 1 is predominant, except in Ghana where all the described isolates were genotype 3. A prospective French study performed between 1999 and 2001 indicated that genotypes 2 and 3 viruses circulated with a significant frequency (10%). Pathogenic properties might not differ according to the genotype. PMID:18387751
Servant-Delmas, A; Laperche, S; Mercier, M; Lefrère, J-J
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
This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of
Javier Cañón; Paolo Alexandrino; Isabel Bessa; Carlos Carleos; Yolanda Carretero; Susana Dunner; Nuno Ferran; David Garcia; Jordi Jordana; Denis Laloë; Albano Pereira; Armand Sanchez; Katayoun Moazami-Goudarzi
Human genetic diversity refers to genomic variation among races, ethnic groups, isolated populations and individuals worldwide, and is one major resource and tool on discovering human evolution and migration, interaction between genetic background and environment, and factors associated with human diseases and health. China has abundant and valuable resource of human genetic diversity due to 56 ethnic groups and a large population accounting for one fifth of the total population in the world. After decades of efforts, a large number of research data on human genetic diversity have been accumulated in China, and some of outcomes reach advanced international level. This review mainly focuses on the recent progress and outcomes achieved in applying genetic markers including morphological markers, biochemical and immunological markers and DNA markers in research of genetic diversity, and the application of mitochondrial DNA, Y chromosomal DNA, HLA and others in research of the origin and relationship of Chinese ethic groups, and the origin and mi-of modern East Asian populations. This review also summarizes the advances in the research fields of preservation and utilization of Chinese genetic resource, identification of genes associated with disease selective and adaptive for natural pressure, application of whole genome association study and next generation sequencing, and Chinese human genome as well. PMID:23208133
Yang, Zhao-Qing; Chu, Jia-You
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
It is clear that genes at the major histocompatibility complex (MHC) are involved in mate preferences in a range of species, including humans. However, many questions remain regarding the MHC's exact influence on mate preference in humans. Some research suggests that genetic dissimilarity and individual genetic diversity (heterozygosity) at the MHC influence mate preferences, but the evidence is often inconsistent
Hanne. C. Lie; Leigh W. Simmons; Gillian Rhodes
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
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
Four featherback fish of the Family Notopteridae in Thailand, Notopterus notopterus, Chitala ornata, Chitala blanci and Chitala lopis, were studied using allozyme electrophoresis to obtain their genetic diversity informations. With a total of 38 enzyme loci screened, 28 variable loci were found of being allelically different between the four species. Of the 28 variable loci, 11 loci ( ADA*, ADH*,
Panom K. Sodsuk; Srirat Sodsuk
Vast germplasm collections are accessible but their use for crop improvement is limited-efficiently accessing genetic diversity is still a challenge. Molecular markers have clarified the structure of genetic diversity in a broad range of crops. Recent developments have made whole-genome surveys and gene-targeted surveys possible, shedding light on population dynamics and on the impact of selection during domestication. Thanks to this new precision, germplasm description has gained analytical power for resolving the genetic basis of trait variation and adaptation in crops such as major cereals, chickpea, grapevine, cacao, or banana. The challenge now is to finely characterize all the facets of plant behavior in carefully chosen materials. We suggest broadening the use of 'core reference sets' so as to facilitate material sharing within the scientific community. PMID:20167531
Glaszmann, J C; Kilian, B; Upadhyaya, H D; Varshney, R K
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
Mandibles from 13 island and six mainland populations of common shrews from the west coast of Scotland were subjected to geometric morphometric analysis in order to investigate the relationship between genetic diversity and fluctuating asymmetry. Although population mean shape fluctuating asymmetry (FA) and size FA were significantly inversely correlated with population genetic diversity this result was substantially due to one island. Sanda, the smallest island with by far the lowest genetic diversity, also had the highest FA. When Sanda was removed from the analysis, the relationship was not significant. There was no relationship between genetic diversity and FA at the individual level, whether measured as mean locus heterozygosity or d(2). In general, if genetic variation affects FA at all, the effect is weak and may only be of biological interest in very small populations. PMID:18194233
White, T A; Searle, J B
Primary production in the open ocean is dominated by the closely related cyanobacterial genera Prochlorococcus and Synechococcus. This thesis explores the relationship between physiological and genetic diversity in cultured isolates of Prochlorococcus and...
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
The fluorescent protein (FP) gene family is a highly diverse group of proteins whose expression govern color diversity in corals. Here, we examine the genetic diversity of FPs and the extent to which it can be used to assess phylogenetic relationships within the coral genus Agaricia. Tissue samples were collected throughout the Florida Keys from a wide range of phenotypes within the genus Agaricia (A. agaricites [n = 7], A. fragilis [n = 13], and A. lamarcki [n = 2]), as well as the confamilial species Helioseris cucullata (n = 3). Primers were developed from published cDNA sequences to amplify a region of coding and noncoding sequences of FPs. Cloning reactions were performed to capture the multiple copies of FPs and allele diversity. In the resulting 116 cloned sequences, we identified a 179-bp coding region for phylogenetic analysis. Three distinct clades were found in all 3 species of Agaricia, potentially representing 3 copies of the FP gene. Of the 3 gene copies, 2 contain distinct subclades that display reciprocal monophyly between A. agaricites and A. fragilis, whereas A. lamarcki is polyphyletic. Further resolution of the species phylogeny is necessary to fully understand how genetic diversity within this gene family is distributed among taxa and habitats. PMID:23667051
Meyers, Meredith; Porter, James W; Wares, John P
Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8?million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations. PMID:23823723
Prado-Martinez, Javier; Sudmant, Peter H; Kidd, Jeffrey M; Li, Heng; Kelley, Joanna L; Lorente-Galdos, Belen; Veeramah, Krishna R; Woerner, August E; O'Connor, Timothy D; Santpere, Gabriel; Cagan, Alexander; Theunert, Christoph; Casals, Ferran; Laayouni, Hafid; Munch, Kasper; Hobolth, Asger; Halager, Anders E; Malig, Maika; Hernandez-Rodriguez, Jessica; Hernando-Herraez, Irene; Prüfer, Kay; Pybus, Marc; Johnstone, Laurel; Lachmann, Michael; Alkan, Can; Twigg, Dorina; Petit, Natalia; Baker, Carl; Hormozdiari, Fereydoun; Fernandez-Callejo, Marcos; Dabad, Marc; Wilson, Michael L; Stevison, Laurie; Camprubí, Cristina; Carvalho, Tiago; Ruiz-Herrera, Aurora; Vives, Laura; Mele, Marta; Abello, Teresa; Kondova, Ivanela; Bontrop, Ronald E; Pusey, Anne; Lankester, Felix; Kiyang, John A; Bergl, Richard A; Lonsdorf, Elizabeth; Myers, Simon; Ventura, Mario; Gagneux, Pascal; Comas, David; Siegismund, Hans; Blanc, Julie; Agueda-Calpena, Lidia; Gut, Marta; Fulton, Lucinda; Tishkoff, Sarah A; Mullikin, James C; Wilson, Richard K; Gut, Ivo G; Gonder, Mary Katherine; Ryder, Oliver A; Hahn, Beatrice H; Navarro, Arcadi; Akey, Joshua M; Bertranpetit, Jaume; Reich, David; Mailund, Thomas; Schierup, Mikkel H; Hvilsom, Christina; Andrés, Aida M; Wall, Jeffrey D; Bustamante, Carlos D; Hammer, Michael F; Eichler, Evan E; Marques-Bonet, Tomas
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 two antigenic subgroups of human respiratory syncytial virus (HRSV). The diversity between HMPV subgroups was greatest for the SH and G proteins (59 and 37% identity, respectively), which were even more divergent than their HRSV counterparts (72 and 55% cross-subgroup identity, respectively). It is reasonable to anticipate that the two genetic subgroups of HMPV represent antigenic subgroups approximately comparable to those of HRSV. PMID:14592754
Biacchesi, Stéphane; Skiadopoulos, Mario H; Boivin, Guy; Hanson, Christopher T; Murphy, Brian R; Collins, Peter L; Buchholz, Ursula J
Quality production of the shrimp Penaeus monodon in hatchery operations depends heavily on the evaluation of genetic diversity and population structure of brood stocks. Mitochondrial DNA (mtDNA) sequences have been widely used to study genetic variability and relationships in many crustacean groups, and these same markers may be incorporated into evaluation studies of shrimp broods and populations. For this purpose we looked at variation in mitochondrial D-loop sequences as an indicator of genetic diversity in shrimp populations from a region of India that represents the main sources of new material for brood stocks. In our study of these populations the overall mean genetic diversity was 0.191. The highest level of genetic diversity (0.357) was observed in the Kakinada population, whereas the lowest diversity (0.0171) was observed in the Nellore population. The results also indicate that overall, the populations along the Andhra Pradesh coast are genetically diverse despite the fact that there is considerable gene flow between them. From the results, it is evident that east cost of India shows high genetic diversity among P. monodon broods and no evidence of loss of diversity due to excessive inbreeding. The fact that the genetic variability of these populations has been maintained, despite ten years of dependence on these broods, shows that at the present time there is no indication of over exploitation. PMID:24363984
Khedkar, Gulab Dattarao; Reddy, A Chandrashekar; Ron, Tetszuan Benny; Haymer, David
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.
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
Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species diversity and genetic diversity interact to influence community structure may be critically important for predicting the consequences of biodiversity loss. PMID:23858643
Crawford, Kerri M; Rudgers, Jennifer A
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
Some introduced populations thrive and evolve despite the presumed loss of diversity at introduction. We aimed to quantify the amount of genetic diversity retained at introduction in species that have shown evidence of adaptation to their introduced environments. Samples were taken from native and introduced ranges of Arctotheca populifolia and Petrorhagia nanteuilii. Using microsatellite data, we identified the source for each introduction, estimated genetic diversity in native and introduced populations, and calculated the amount of diversity retained in introduced populations. These values were compared to those from a literature review of diversity in native, confamilial populations and to estimates of genetic diversity retained at introduction. Gene diversity in the native range of both species was significantly lower than for confamilials. We found that, on average, introduced populations showing evidence of adaptation to their new environments retained 81% of the genetic diversity from the native range. Introduced populations of P. nanteuilii had higher genetic diversity than found in the native source populations, whereas introduced populations of A. populifolia retained only 14% of its native diversity in one introduction and 1% in another. Our literature review has shown that most introductions demonstrating adaptive ability have lost diversity upon introduction. The two species studied here had exceptionally low native range genetic diversity. Further, the two introductions of A. populifolia represent the largest percentage loss of genetic diversity in a species showing evidence of substantial morphological change in the introduced range. While high genetic diversity may increase the likelihood of invasion success, the species examined here adapted to their new environments with very little neutral genetic diversity. This finding suggests that even introductions founded by small numbers of individuals have the potential to become invasive.
Rollins, Lee A; Moles, Angela T; Lam, Serena; Buitenwerf, Robert; Buswell, Joanna M; Brandenburger, Claire R; Flores-Moreno, Habacuc; Nielsen, Knud B; Couchman, Ellen; Brown, Gordon S; Thomson, Fiona J; Hemmings, Frank; Frankham, Richard; Sherwin, William B
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.
ISSR was applied to detect the relationship between 16 Cymbidium species, and 836 bands were amplified with 15 primers, including 227 polymorphic bands. The polymorphic percentage is 27.2%. UPGMA results showed that the genetic distance were closest between C.goeringii (Rchb.f.) Rchb.f. and C. goeringii var. longibracteatum, and C.lancifolium Hook. was far away from the other 15 species. This result is quite similar to the traditional classification, indicating that the technique could supplement some information to traditional taxonomy in the molecular level. PMID:18487154
Wu, Zhen-Xing; Wang, Hui-Zhong; Shi, Nong-Nong; Zhao, Yan
Plague outbreaks are occasionally reported in Brazil. Unfortunately, due to great genetic similarity, molecular subtyping of Yersinia pestis strains is difficult. Analysis of multiple-locus variable number of tandem repeats (VNTR), also known as MLVA, has been found to be a valuable tool to discriminate among strains. To check for genetic differences, strains obtained from two different ecological complexes in Brazil collected during two different epidemiological events, an epizootic in Sítio Alagoinha in 1967 and an outbreak in Planalto da Borborema in 1986, were subtyped through MLVA using 12 VNTR loci. Three clusters (A, B and C) were observed. Of the 20 strains from the epizootic, 18 fit into cluster A. Cluster A was divided into two subgroups: A(1) (15 strains) and A(2) (3 strains). Of the 17 strains from the outbreak, 15 fit into cluster B. Cluster B was divided into three subgroups: B(1) (4 strains), B(2) (4 strains) and B(3) (7 strains). Cluster C is a singleton with one epizootic strain. The external standards, Y. pestis CO92 and Y. pseudotuberculosis IP32953, formed two clusters of singletons. The stability of 12 VNTR loci of three unrelated cultures included in this study was assessed. The 12 VNTR loci were stable through multiple serial subcultures in the laboratory. MLVA revealed that Y. pestis populations in Brazil are not monomorphic, and that there is intraspecific genetic diversity among Brazilian plague strains. We conclude that there is some correlation among genetic groups of this species, related to the temporal and geographic origin of isolates. PMID:23079835
Oliveira, M B M; Barros, M P S; Silveira-Filho, V M; Araújo-Nepomuceno, M R; Balbino, V Q; Leal, N C; Almeida, A M P; Leal-Balbino, T C
The application of hypervariable minisatellite genomic families to the reconstruction of population genetic structure holds great promise in describing the demographic history and future prospects of free-ranging populations. This potential has not yet been realized due to unforeseen empirical constraints associated with the use of heterologous species probes, to theoretical limitations on the power of the procedure to track genic heterozygosity and kinship, and to the absence of extensive field studies to test genetic predictions. We combine here the technical development of feline-specific VNTR (variable number tandem repeat) families of genetic loci with the long-term demographic and behavioral observations of lion populations of the Serengeti ecosystem in East Africa. Minisatellite variation was used to quantify the extent of genetic variation in several populations that differed in their natural history and levels of inbreeding. Definitive parentage, both maternal and paternal, was assessed for 78 cubs born in 11 lion prides, permitting the assessment of precise genealogical relationships among some 200 lions. The extent of DNA restriction fragment sharing between lions was empirically calibrated with the coefficient of relatedness, r, in two different populations that had distinct demographic histories. The results suggest that reliable estimates of relative genetic diversity, of parentage, and of individual relatedness can be achieved in free-ranging populations, provided the minisatellite family is calibrated in established pedigrees for the species. PMID:1940281
Gilbert, D A; Packer, C; Pusey, A E; Stephens, J C; O'Brien, S J
Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods). The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total) was found for Spirogyra (41 NHS) and for each clade (totaling 73 NHS). This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.
The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes.
Fukunaga, Kenji; Hill, Jason; Vigouroux, Yves; Matsuoka, Yoshihiro; Sanchez G., Jesus; Liu, Kejun; Buckler, Edward S.; Doebley, John
Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.
Sullender, Wayne M.
Aims Platycladus orientalis (Cupressaceae) is an old-growth tree species which distributed in the imperial parks and ancient temples in Beijing, China. We aim to (1) examine the genetic diversity and reproductive traits of old-growth and young populations of P. orientalis to ascertain whether the older populations contain a higher genetic diversity, more private alleles and a higher reproductive output compared with younger populations; (2) determine the relationships between the age of the population and the genetic diversity and reproductive traits; and (3) determine whether the imperial parks and ancient temples played an important role in maintaining the reproductive capacity and genetic diversity of Platycladus orientalis. Methods Samples from seven young (younger than 100 yrs.) and nine old-growth (older than 300 yrs.) artificial populations were collected. For comparison, three young and two old-growth natural populations were also sampled. Nine microsatellite loci were used to analyze genetic diversity parameters. These parameters were calculated using FSTAT version 2.9.3 and GenAlex v 6.41. Important Findings The old-growth artificial populations of P. orientalis have significantly higher genetic diversity than younger artificial populations and similar levels to those in extant natural populations. The imperial parks and ancient temples, which have protected these old-growth trees for centuries, have played an important role in maintaining the genetic diversity and reproductive capacity of this tree species.
Zhu, Lin; Lou, Anru
Understanding factors that determine heterogeneity in levels of parasitism across individuals is a major challenge in disease ecology. It is known that genetic makeup plays an important role in infection likelihood, but the mechanism remains unclear as does its relative importance when compared to other factors. We analyzed relationships between genetic diversity and macroparasites in outbred, free-ranging populations of raccoons (Procyon lotor). We measured heterozygosity at 14 microsatellite loci and modeled the effects of both multi-locus and single-locus heterozygosity on parasitism using an information theoretic approach and including non-genetic factors that are known to influence the likelihood of parasitism. The association of genetic diversity and parasitism, as well as the relative importance of genetic diversity, differed by parasitic group. Endoparasite species richness was better predicted by a model that included genetic diversity, with the more heterozygous hosts harboring fewer endoparasite species. Genetic diversity was also important in predicting abundance of replete ticks (Dermacentor variabilis). This association fit a curvilinear trend, with hosts that had either high or low levels of heterozygosity harboring fewer parasites than those with intermediate levels. In contrast, genetic diversity was not important in predicting abundance of non-replete ticks and lice (Trichodectes octomaculatus). No strong single-locus effects were observed for either endoparasites or replete ticks. Our results suggest that in outbred populations multi-locus diversity might be important for coping with parasitism. The differences in the relationships between heterozygosity and parasitism for the different parasites suggest that the role of genetic diversity varies with parasite-mediated selective pressures.
Ruiz-Lopez, Maria Jose; Monello, Ryan J.; Gompper, Matthew E.; Eggert, Lori S.
Understanding factors that determine heterogeneity in levels of parasitism across individuals is a major challenge in disease ecology. It is known that genetic makeup plays an important role in infection likelihood, but the mechanism remains unclear as does its relative importance when compared to other factors. We analyzed relationships between genetic diversity and macroparasites in outbred, free-ranging populations of raccoons (Procyon lotor). We measured heterozygosity at 14 microsatellite loci and modeled the effects of both multi-locus and single-locus heterozygosity on parasitism using an information theoretic approach and including non-genetic factors that are known to influence the likelihood of parasitism. The association of genetic diversity and parasitism, as well as the relative importance of genetic diversity, differed by parasitic group. Endoparasite species richness was better predicted by a model that included genetic diversity, with the more heterozygous hosts harboring fewer endoparasite species. Genetic diversity was also important in predicting abundance of replete ticks (Dermacentor variabilis). This association fit a curvilinear trend, with hosts that had either high or low levels of heterozygosity harboring fewer parasites than those with intermediate levels. In contrast, genetic diversity was not important in predicting abundance of non-replete ticks and lice (Trichodectes octomaculatus). No strong single-locus effects were observed for either endoparasites or replete ticks. Our results suggest that in outbred populations multi-locus diversity might be important for coping with parasitism. The differences in the relationships between heterozygosity and parasitism for the different parasites suggest that the role of genetic diversity varies with parasite-mediated selective pressures. PMID:23049796
Ruiz-López, María José; Monello, Ryan J; Gompper, Matthew E; Eggert, Lori S
The Genetic Relationship of the Ainu Language.by James Patrie Oceanic Linguistics Special Publication #17. Honolulu: University of Hawaii Press, 1982. 174 pp. Map, Bibliography, Index of Ainu Forms. $7.50 (paper)
J. Marshal Unger
Mycobacterium avium, one of the species of the M. avium complex (MAC), includes 4 subspecies, i.e., M. avium subsp. hominissuis (MAH), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS) and M. avium subsp. paratuberculosis (MAP), in turn classified into the S (sheep) and C (cattle) types. These subspecies, although closely related, represent distinct organisms, each endowed with specific pathogenetic and host range characteristics, ranging from environmental opportunistic bacteria that cause infections in swine and immunocompromised patients to pathogens of birds and ruminants. The present review summarizes the basic epidemiological and pathological features of the M. avium subspecies, describes the major genomic events responsible of M. avium subspecies diversity (insertion sequences, sequence variations in specific chromosome loci or genes, deletions, duplications and insertions of large genomic regions) and then reconstructs the phylogenetic relationships among the M. avium subspecies. PMID:24345519
Rindi, Laura; Garzelli, Carlo
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
Eighteen allozyme loci were used to examine genetic diversity in 10 natural populations of Sarracenia leucophylla Raf., a pitcher plant restricted to the southeastern United States. One ex situ population propagated for restoration in Georgia was also analyzed. S. leucophylla is an insect-pollinated, outcrossing perennial wetland herb that is threatened over much of its geographic range. Fifteen loci (83.3%) were polymorphic, with a mean number of alleles of 3.33. Compared to species having similar life-history traits and to previously analyzed Sarracenia species, S. leucophylla displayed unexpectedly high genetic diversity. For example, genetic diversity within the species (Hes) was 0.224 and mean population genetic diversity (Hep) was 0.183. Although small S. leucophylla populations maintained less genetic diversity than larger ones, these differences were not statistically significant. Nonetheless, this suggests that small populations may have lost rare alleles. Statistically significant genetic differentiation among populations was found (theta = 0.192, P < .01), although it was not atypical considering the species' life-history characteristics. A significant correlation (P < .01) between genetic and geographic distance was found, indicating an isolation-by-distance effect. However, the correlation coefficient for this relationship was low (r = 0.46), suggesting that factors other than gene flow play a prominent role in the geographic distribution of genetic diversity within the species. The ex situ population captured most of the allozyme variation found in its source population. PMID:15220390
Wang, Z-F; Hamrick, J L; Godt, M J W
Parasitic nematodes show levels of genetic diversity comparable to other taxa, but the functional conse- quences of this are not understood. Thus, a large body of theoretical work highlights the potential conse- quences 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
S. Paterson; M. E. Viney
The cyanobionts isolated from 10 Azolla accessions belonging to 6 species (Azolla mexicana, A. microphylla, A. rubra, A. caroliniana, A. filiculoides, A. pinnata) were cultured under laboratory conditions and analyzed on the basis of whole cell protein profiles and molecular marker dataset generated using repeat sequence primers (STRR(mod) and HipTG). The biochemical and molecular marker profiles of the cyanobionts were compared with those of the free-living cyanobacteria and symbiotic Nostoc strains from Anthoceros sp., Cycas sp. and Gunnera monoika. Cluster analysis revealed the genetic diversity among the selected strains, and identified 3 distinct clusters. Group 1 included cyanobionts from all the 10 accessions of Azolla, group 2 comprised all the symbiotic Nostoc strains, while group 3 included the free-living cyanobacteria belonging to the genera Nostoc and Anabaena. The interrelationships among the Azolla cyanobionts were further revealed by principal component analysis. Cyanobionts from A. caroliniana-A. microphylla grouped together while cyanobionts associated with A. mexicana-A. filiculoides along with A. pinnata formed another group. A. rubra cyanobionts had intermediate relationship with both the subgroups. This is the first study analyzing the diversity existing among the cultured cyanobionts of diverse Azolla species through the use of biochemical and molecular profiles and also the genetic distinctness of these free-living cyanobionts as compared to cyanobacterial strains of the genera Anabaena and Nostoc. PMID:18481216
Sood, A; Prasanna, R; Prasanna, B M; Singh, P K
In this review, we first analyse the objectives to consider in preserving diversity, fitness and adaptability of farm animal\\u000a genetic resources (AnGR), given the links between genetic diversity and fitness-adaptedness (FA) traits. Ways to measure diversity\\u000a are then presented, and tools available for managing genetic diversity within given economic constraints are described, under\\u000a a theoretical framework proposed by Martin Weitzman.
Louis Ollivier; Jean-Louis Foulley
The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS(®), to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System. PMID:21429115
Vandergast, Amy G; Perry, William M; Lugo, Roberto V; Hathaway, Stacie A
The genetic diversity and structure of horses raised in France were investigated using 11 microsatellite markers and 1679 animals belonging to 34 breeds. Between-breed differences explained about ten per cent of the total genetic diversity (Fst = 0.099). Values of expected heterozygosity ranged from 0.43 to 0.79 depending on the breed. According to genetic relationships, multivariate and structure analyses, breeds could be classified into four genetic differentiated groups: warm-blooded, draught, Nordic and pony breeds. Using complementary maximisation of diversity and aggregate diversity approaches, we conclude that particular efforts should be made to conserve five local breeds, namely the Boulonnais, Landais, Merens, Poitevin and Pottok breeds.
A total of 495 individuals from five different Argentinian tribes was examined for variation in 23 blood group and protein genetic systems, and the results were integrated with previous data on some of these systems. These tribes generally present RH * R1, PGM1 * 1, and ACP * A frequencies lower and RH * R2, ESD * 1, and GLO * 1 prevalences higher than those observed in other South American Indian groups. Earlier studies with mitochondrial DNA showed that haplogroup A was present in low frequencies in these tribes, but haplogroup B showed a high prevalence among the Mataco. Average heterozygosities are very similar in the five tribes, while estimates of non-Indian ancestry are generally low. Both the blood group and protein, as well as the mtDNA data sets, divide the five tribes into two groups, and the relationships obtained with the blood group and protein systems are exactly those expected on the basis of geography and language. However, the topology obtained with the mtDNA results was different, possibly due to sampling effects or diverse patterns of exchange between the groups related to sex. PMID:11385600
Goicoechea, A S; Carnese, F R; Dejean, C; Avena, S A; Weimer, T A; Franco, M H; Callegari-Jacques, S M; Estalote, A C; Simões, M L; Palatnik, M; Salzano, F M
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
Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species. PMID:24129175
Qian, Xin; Wang, Cai-xia; Tian, Min
Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species.
Qian, Xin; Wang, Cai-xia; Tian, Min
Background and Aims Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. Methods The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Key Results Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. Conclusions This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.
Diez, Concepcion M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis
We examine the degree to which ethnic diversity in social networks relates to the frequency of interethnic romantic relationships for 318 college students. In a multi-nomial logit, we find that the odds of having an interethnic relationship once or twice, versus never, increase significantly if the respondent has a relatively ethnically diverse…
Clark-Ibanez, Marisol; Felmlee, Diane
Polyandry is common in many species and it has been suggested that females engage in multiple mating to increase the genetic diversity of their offspring (genetic diversity hypothesis). Multiple paternity occurs in 30% of litters in wild populations of house mice, Mus musculus musculus, and multiple-sired litters are genetically more diverse than single-sired ones. Here, we aimed to test whether female house mice produce multiple-sired litters when they have the opportunity to produce genetically diverse litters. We assessed the rates of multiple paternity when females could choose to mate with two males that were genetically dissimilar to each other (i.e. nonsiblings and MHC dissimilar) compared with when females could choose to mate with two males that were genetically similar to each other (i.e. siblings and shared MHC alleles). Multiple mating may depend upon a female's own condition, and, therefore, we also tested whether inbred (from full-sibling matings) females were more likely to produce multiple-sired progeny than outbred controls. Overall we found that 29% of litters had multiple sires, but we found no evidence that females were more likely to produce multiple-sired litters when they had the opportunity to mate with genetically dissimilar males compared with controls, regardless of whether females were inbred or outbred. Thus, our findings do not support the idea that female mice increase multiple paternity when they have the opportunity to increase the genetic diversity of their offspring, as expected from the genetic diversity hypothesis.
Thonhauser, Kerstin E.; Raveh, Shirley; Penn, Dustin J.
In Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus. PMID:23985385
Konyaev, Sergey V; Yanagida, Tetsuya; Nakao, Minoru; Ingovatova, Galina M; Shoykhet, Yakov N; Bondarev, Alexandr Y; Odnokurtsev, Valeriy A; Loskutova, Kyunnyay S; Lukmanova, Gulnur I; Dokuchaev, Nikolai E; Spiridonov, Sergey; Alshinecky, Mikhail V; Sivkova, Tatyana N; Andreyanov, Oleg N; Abramov, Sergey A; Krivopalov, Anton V; Karpenko, Sergey V; Lopatina, Natalia V; Dupal, Tamara A; Sako, Yasuhito; Ito, Akira
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.
Eula Maria de M. B., Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valeria de, Oliveira; Marilia, Oliveira; Elda, Bueno; Silvana, Petrofeza
Restriction site amplified polymorphism (RSAP) was used, for the first time, to analyze the genetic structure and diversity of four, mainly cultivated, varieties of the brown alga, Saccharina japonica. Eighty-eight samples from varieties " Rongfu ", " Fujian ", " Ailunwan " and " Shengchanzhong " were used for the genetic analyses. One hundred and ninety-eight bands were obtained using eight combinations of primers. One hundred and ninety-one (96.46%) were polymorphic bands. Nei's genetic diversity was 0.360, and the coefficient of genetic differentiation was 0.357. No inbreeding-type recession was found in the four brown alga varieties and the results of the " Ailunwan " variety using samples from 2 years showed that the variety was becoming less diverse during the selection inherent in the breeding program. Genetic diversity and cluster analyses results were consistent with these genetic relationships. The results show the RSAP method is suitable for genetic analysis. Continuous inbreeding and selection could reduce the genetic diversity effectively; therefore periodical supervision is required.
Zhao, Cui; Liu, Cui; Li, Wei; Chi, Shan; Feng, Rongfang; Liu, Tao
The objectives of this study were firstly, to determine the genetic diversity of Monilinia laxa isolates from Hungary, using the PCR-based inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) technique; secondly, to prepare genetic diversity groups based on the dendrograms; and finally, to select some relevant isolates to study their fungicide sensitivity. 55 and 77 random amplified polymorphic ISSR and RAPD markers, of which 23 and 18 were polymorphic and 32 and 59 monomorphic, respectively, were used to assess the genetic diversity and to study the structure of M. laxa populations in Hungary. 27 isolates out of 57 ones were confirmed as M. laxa from several orchards (subpopulations) in three geographical regions, in various inoculum sources and in various hosts, were used. 10 fungicides and 12 isolates selected from genetic diversity groups based on the ISSR dendrograms were used to determine the fungicide sensitivity of the selected isolates. The analysis of population structure revealed that genetic diversity within locations, inoculum sources and host (H(S)) accounted for 99 % of the total genetic diversity (H(T)), while genetic diversity among locations, inoculum sources and host represented only 1 %. The relative magnitude of gene differentiation between subpopulations (G(ST)) and the estimate of the number of migrants per generation (Nm) averaged 0.005-0.009 and 53.9-99.2, respectively, for both ISSR and RAPD data set. The results obtained in dendrograms were in accordance with the gene diversity analysis. Grouping of isolates in the dendrograms was irrespective of whether they came from the same or different geographical locations. There was no relationship between clustering among isolates from inoculum sources and hosts. In the fungicide sensitivity tests, five isolates out of 12 were partly insensitive to boscalid+piraclostrobin, cyprodinil, fenhexamid or prochloraz. Obtained results in genetic diversity of M. laxa populations are discussed together with implications for the management of brown rot. PMID:24474390
Fazekas, Mónika; Madar, Anett; Sipiczki, Matthias; Miklós, Ida; Holb, Imre J
Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102
Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E
Background Evolution has resulted in large repertoires of olfactory receptor (OR) genes, forming the largest gene families in mammalian genomes. Knowledge of the genetic diversity of olfactory receptors is essential if we are to understand the differences in olfactory sensory capability between individuals. Canine breeds constitute an attractive model system for such investigations. Results We sequenced 109 OR genes considered representative of the whole OR canine repertoire, which consists of more than 800 genes, in a cohort of 48 dogs of six different breeds. SNP frequency showed the overall level of polymorphism to be high. However, the distribution of SNP was highly heterogeneous among OR genes. More than 50% of OR genes were found to harbour a large number of SNP, whereas the rest were devoid of SNP or only slightly polymorphic. Heterogeneity was also observed across breeds, with 25% of the SNP breed-specific. Linkage disequilibrium within OR genes and OR clusters suggested a gene conversion process, consistent with a mean level of polymorphism higher than that observed for introns and intergenic sequences. A large proportion (47%) of SNP induced amino-acid changes and the Ka/Ks ratio calculated for all alleles with a complete ORF indicated a low selective constraint with respect to the high level of redundancy of the olfactory combinatory code and an ongoing pseudogenisation process, which affects dog breeds differently. Conclusion Our demonstration of a high overall level of polymorphism, likely to modify the ligand-binding capacity of receptors distributed differently within the six breeds tested, is the first step towards understanding why Labrador Retrievers and German Shepherd Dogs have a much greater potential for use as sniffer dogs than Pekingese dogs or Greyhounds. Furthermore, the heterogeneity in OR polymorphism observed raises questions as to why, in a context in which most OR genes are highly polymorphic, a subset of these genes is not? This phenomenon may be related to the nature of their ligands and their importance in everyday life.
Robin, Stephanie; Tacher, Sandrine; Rimbault, Maud; Vaysse, Amaury; Dreano, Stephane; Andre, Catherine; Hitte, Christophe; Galibert, Francis
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
Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe. PMID:24533164
Teixeira, Helena; Rodríguez-Echeverría, Susana; Nabais, Cristina
Juniperus thurifera L. is an important tree endemic to the western Mediterranean basin that it is able to grow in semi-arid climates. It nowadays exhibits a disjunct distribution pattern, occurring in North Africa, Spain, France and the Italian Alps. The Strait of Gibraltar has acted as an efficient barrier against gene flow between African and European populations, which are considered different subspecies by some authors. We aimed at describing the intraspecific genetic diversity of J. thurifera in populations from the Iberian Peninsula and Morocco and the phylogeographical relationships among these populations. The ploidy level of J. thurifera was examined and eleven nuclear microsatellites (nSSRs) developed for J. thurifera were assessed for genotyping this species. Six nSSRs were polymorphic and subsequently used to assess the genetic diversity and structure of the studied populations. Genotyping of the tetraploid J. thurifera using nuclear microsatellites supports the separation of Moroccan and Spanish populations into two genetically differentiated groups that correspond to the proposed subspecies africana and thurifera. High values of within population genetic diversity were found, that accounted for 90% of the total genetic variance, while population structure was weak. The estimators of genetic diversity were higher in populations of Spain than in populations of Morocco pointing for a possible loss of genetic diversity during the spread of this species to Africa from Europe.
Teixeira, Helena; Rodriguez-Echeverria, Susana; Nabais, Cristina
Introduction: In the departments of the Vaupés and Guaviare, in southeastern Colombia, in a transitional area between Amazonia and the eastern plains, inhabit indigenous groups belonging to the Tukanoan (East) and Guahiban linguistic families. Although some studies have dealt with the culture and the cosmology description of these groups, little research has been done on the biological diversity and genetic relationships of such groups. Objective: To estimate the diversity, the structure, and the genetic relationships of one Guahiban and two Tukanoan groups of the Colombian Amazonian region. Methods: Samples were collected (n = 106) from unrelated individuals belonging to the Vaupés native indigenous communities. The DNA was extracted and nine autosomal microsatellites were typed. Several measures of diversity, FST, pairwise FST, and population differentiation between groups were calculated. Finally, it was estimated the genetic distances of the groups studied in relation with other Amazonian, Andean and Central American indigenous people. Results: 1. The genetic diversity found stands within the range of other Amazonian populations, whereas compared to the mestizo and afro-descendant Colombian populations, such diversity showed to be lower. 2. The structure and population differentiation tests showed two clusters; one consisting of the Vaupés Tukanoan and Guaviare Tukanoan groups, and a second one formed by the Guayabero. 3. Tukanoan groups are found to be closer related to the Brazilian Amazonian populations than to the Guayabero. Conclusion: The results of this study suggest that the Guayabero group from Guaviare, are genetically differentiated from those Tukanoan groups of the Vaupés and Guaviare.
Braga, Yamid; Arias B, Leonardo
The pattern of genetic variation within and among natural populations of broomrape (Orobanche crenata Forsk.) from southern Spain was analysed by RAPD markers. Hierarchical analysis of phenotypic diversity using AMOVA was performed\\u000a to analyse the partitioning of the variation among populations and among individuals. Although most of the genetic diversity\\u000a was attributable to differences among individuals within a population (94.29%),
B. Román; D. Rubiales; A. M. Torres; J. I. Cubero; Z. Satovic
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
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
Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods. PMID:24336928
Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A
BACKGROUND: The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial
Ross DE MacPhee; Alexei N Tikhonov; Dick Mol; Alex D Greenwood
Genetic diversity is supposed to support the colonization success of expanding species, in particular in situations where microsite availability is constrained. Addressing the role of genetic diversity in plant invasion experimentally requires its manipulation independent of propagule pressure. To assess the relative importance of these components for the invasion of Senecio vernalis, we created propagule mixtures of four levels of genotype diversity by combining seeds across remote populations, across proximate populations, within single populations and within seed families. In a first container experiment with constant Festuca rupicola density as matrix, genotype diversity was crossed with three levels of seed density. In a second experiment, we tested for effects of establishment limitation and genotype diversity by manipulating Festuca densities. Increasing genetic diversity had no effects on abundance and biomass of S. vernalis but positively affected the proportion of large individuals to small individuals. Mixtures composed from proximate populations had a significantly higher proportion of large individuals than mixtures composed from within seed families only. High propagule pressure increased emergence and establishment of S. vernalis but had no effect on individual growth performance. Establishment was favoured in containers with Festuca, but performance of surviving seedlings was higher in open soil treatments. For S. vernalis invasion, we found a shift in driving factors from density dependence to effects of genetic diversity across life stages. While initial abundance was mostly linked to the amount of seed input, genetic diversity, in contrast, affected later stages of colonization probably via sampling effects and seemed to contribute to filtering the genotypes that finally grew up. In consequence, when disentangling the mechanistic relationships of genetic diversity, seed density and microsite limitation in colonization of invasive plants, a clear differentiation between initial emergence and subsequent survival to juvenile and adult stages is required.
Erfmeier, Alexandra; Hantsch, Lydia; Bruelheide, Helge
Reviews current research on a woman's chances of bearing twins and the genetic relationship, prenatal competition, and personality similarities between twins. In addition, the nature/nurture controversy is discussed in terms of evidence from studies of identical twins reared apart. Future studies are suggested to discover the ways twinning might…
Lethal Yellowing (LY) is one the main diseases affecting coconut worldwide, making the research for resistant germplasm vital to production. Study objectives were to: (i) estimate diversity and genetic structure within four commercial Mexican ecotypes and five imported ecotypes; (ii) analyze the genetic relationships between Mexican ecotypes and the main coconut gene pools identified worldwide; and (iii) measure the correlation
Daniel Zizumbo-Villarreal; Mariana Ruiz-Rodriguez; Hugh Harries; Patricia Colunga-GarcíaMarín
Five indigenous Spanish breeds of sheep, Churra, Latxa, Manchega, Rasa-Aragonesa and Merino, with Awassi sheep as a reference breed were genotyped for 19 DNA microsatellites. Allele frequencies and mean heterozygosities revealed the greatest genetic variation in Merino sheep and the lowest in Awassis. Differences in variability were not great in the other breeds studied. The dendrograms obtained based on genetic distances showed a large differentiation between Awassi sheep and the Spanish breeds, as was to be expected from their distinct genetic origin. Merinos appeared separated from the other four breeds, of which, according to a classification based on the fleece characteristics, Churra and Latxa belong to the churro type and Manchega and Rasa-Aragonesa to the so called entrefino type, though no clear separation was evident between the two types. These results suggest that morphological data alone are insufficient for determining relationships between breeds and that studies involving genetic markers may be of great assistance. PMID:9883504
Arranz, J J; Bayón, Y; San Primitivo, F
South Africa has a rich flora which exhibits among the highest species density in the world, distributed across nine biomes\\u000a that support an impressive diversity of animal life. However, a variety of human actions, invasion by alien species, natural\\u000a disturbances and climate change collectively impact negatively on the great diversity of both plant and animal species. In situ conservation has
Patricia Berjak; Paul Bartels; Erica E. Benson; Keith Harding; David J. Mycock; Norman W. Pammenter; Sershen; James Wesley-Smith
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
This study was undertaken to determine the genetic structure, evolutionary relationships, and the genetic diversity among 18 local cattle breeds from Spain, Portugal, and France using 16 microsatellites. Heterozygosities, estimates of Fst, genetic distances, multivariate and diversity analyses, and assignment tests were performed. Heterozygosities ranged from 0.54 in the Pirenaica breed to 0.72 in the Barrosã breed. Seven percent of the total genetic variability can be attributed to differences among breeds (mean Fst = 0.07; P < 0.01). Five different genetic distances were computed and compared with no correlation found to be significantly different from 0 between distances based on the effective size of the population and those which use the size of the alleles. The Weitzman recursive approach and a multivariate analysis were used to measure the contribution of the breeds diversity. The Weitzman approach suggests that the most important breeds to be preserved are those grouped into two clusters: the cluster formed by the Mirandesa and Alistana breeds and that of the Sayaguesa and Tudanca breeds. The hypothetical extinction of one of those clusters represents a 17% loss of diversity. A correspondence analysis not only distinguished four breed groups but also confirmed results of previous studies classifying the important breeds contributing to diversity. In addition, the variation between breeds was sufficiently high so as to allow individuals to be assigned to their breed of origin with a probability of 99% for simulated samples.
Canon, Javier; Alexandrino, Paolo; Bessa, Isabel; Carleos, Carlos; Carretero, Yolanda; Dunner, Susana; Ferran, Nuno; Garcia, David; Jordana, Jordi; Laloe, Denis; Pereira, Albano; Sanchez, Armand; Moazami-Goudarzi, Katayoun
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
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
In order to evaluate the germplasm resources of Pampus argenteus silver pomfret, the genetic diversity and population structure of 132 silver pomfret samples collected from the three regions (the East China Sea, the Yellow Sea and the Bohai Sea) were examined using 13 polymorphic microsatellite loci. Results indicated a high level of genetic diversity. The total number of observed alleles was 68, the mean allele number was 5.46 per locus, and the mean number of effective alleles was 4.91. The polymorphism information content ranged from 0.58 to 0.88. For the 13 polymorphic microsatellite loci, the results of analysis of molecular variance indicated that 92.45% of the genetic variation was contained within populations. Unweighted pair group method with arithmetic mean cluster analysis revealed significant genealogical branches or clusters corresponding to sampling localities. We concluded that there was high genetic diversity in these silver pomfret populations, and that this diversity was related to the complex environment. These results would contribute to important knowledge of genetic diversity and population structure, which would be crucial for establishing appropriate fishery management stocks for this species. PMID:24301952
Qin, Y; Shi, G; Sun, Y
In this study, the samples were collected from nine ETPs and soil contaminated with petroleum products. The genetic diversity of 30 Stenotrophomonas isolates was demonstrated by phylogenetic analysis of their 16S rRNA gene nucleotide sequences, and randomly amplified polymorphic DNA (RAPD) analysis supplemented with in silico signature and restriction enzyme (REs--AluI, BfaI, DpnII, HaeIII, RsaI and Tru9I) digestion analyses. Genetic diversity based on nucleotide sequence data revealed distinct clusters. Functional diversity was analysed on the basis of the abilities of these isolates to degrade phenol, p-cresol, catechol, 4-methylcatechol and hydroquinone. Based on the environmental, genetic and functional diversities, a consortium of mixed defined microbes has been proposed for bioremediation programs. PMID:20554196
Verma, Vinita; Raju, Sajan C; Kapley, Atya; Kalia, Vipin Chandra; Daginawala, Hatim F; Purohit, Hemant J
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
To assess the genetic status of this species, the genetic diversity of wild Macrobrachium nipponense from seven geographic locations in the Yellow River basin were investigated using 20 polymorphic microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity (H) and the expected H, which was arranged from 2 to 10, from 0.4705 to 0.5731, and from 0.5174 to 0.6146, respectively. Hardy-Weinberg equilibrium analysis indicated that a deficiency of heterozygotes existed in all seven populations. Both the F(ST) and AMOVA analyses showed that there is significant difference on population differentiation among populations. The UPGMA clustering tree demonstrated that their close relationship is consistent with their geographic proximity. The data suggest that this Yellow River population has a wide genetic base that is suitable for breeding. PMID:24301938
Qiao, H; Lv, D; Jiang, S F; Sun, S M; Gong, Y S; Xiong, Y W; Jin, S B; Fu, H T
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.
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
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.
We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at\\u000a a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes\\u000a were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles\\u000a were distinguished by the 21 microsatellite markers
A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat
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
Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3' nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism. PMID:23115283
Pita, Justin S; Roossinck, Marilyn J
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
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.
Lowland tropical habitats harbour an unexplored genetic diversity of epiphyllous fungi. In the shade of rainforest understoreys, lichenized fungi are specialized to an ephemeral habitat where they produce little vegetative biomass and develop reproductive structures early. In a first population genetic study of epiphyllous lichen fungi, we analysed the intraspecific genetic diversity of five leaf-colonizing lichen mycobiont species. Sampling focused on a lowland perhumid forest plot in Costa Rica, with additional collections from other localities throughout the country. In all species we detected sympatric occurrence of highly diverged haplotypes. Haplotypes belonging to distinct clades in networks were also found on the same leaf, clearly indicating multiple independent colonization events on single leaves. Despite the unusually high genetic diversity of these leaf-colonizing tropical fungi, we did not detect pronounced spatial structure of the haplotype distribution between geographical regions. The observed patterns suggest that the diversity of foliicolous lichens could be much higher than expected, with several cryptic genetic lineages within each morphologically characterized species. PMID:19389164
Baloch, Elisabeth; Grube, Martin
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.
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.
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
The local geese in the transition region between the Caucasus Mountains and Anatolia have economically significant differences in productivity and are identified by four feather colors, white, black, piebald, and yellow. This study was undertaken to determine the genetic structure, evolutionary relationships, and genetic diversity among these birds. DNA samples were obtained from 100 animals, and 50 random primers were screened. Genetic relationships were determined by random amplified polymorphic DNA polymorphisms obtained from a total of 48 loci, showing 40 bands (83.33%) that were polymorphic among all the populations investigated. A dendrogram constructed for this study revealed a close relationship between the white and the black birds. Additionally, the piebald birds showed close similarity to white and black geese, and the yellow birds displayed a clear distance from the other three populations. PMID:17588148
Devrim, Alparslan Kadir; Kaya, Necati; Guven, Aysel; Kocer, Buket
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
KEYWORDS Population genetics; HLA antigens; genetic relationship; Gurkha population ABSTRACT Indian population is well known for its genetic diversity. Among the numerous endogamous ethnic groups of North Bengal, we have collected blood samples from 50 unrelated Nepali speaking individuals, belonging to Gurkha community. In the present investigation, the frequency of HLA-A and B loci antigens has been analyzed serologically and
Monojit Debnath; Tapas K. Chaudhuri
The genetic diversity in Tunisian fig (Ficus carica L.) was studied using RAPD markers. Thirty-five fig cultivars originating from diverse geographical areas and belonging to three collections were analysed. Random decamer primers were screened to assess their ability to detect polymorphisms in this crop. Forty-four RAPD markers were revealed and used to survey the genetic diversity and to detect cases of mislabelling. As a result, considerable genetic diversity was detected among the studied F. carica accessions. The relationships among the 35 varieties were studied by cluster analysis. The dendrogram showed two main groups composed of cultivars with similar geographic origin. Moreover, the male accessions (caprifigs) were clustered indistinctively within the female ones, suggesting a narrow genetic diversity among these accessions. Our data proved that RAPD markers are useful for germplasm discrimination as well as for investigation of patterns of variation in fig. Since this designed procedure has permitted to establish a molecular database of the reference collections, the opportunity of this study is discussed in relation to the improvement and rational management of fig germplasm. PMID:17362329
Salhi-Hannachi, Amel; Chatti, Khaled; Saddoud, Olfa; Mars, Messaoud; Rhouma, Abdelmajid; Marrakchi, Mohamed; Trifi, Mokhtar
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
The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus. PMID:21735103
Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi
Background Invasions of natural communities by non-indigenous species are currently rated as one of the most important global-scale threats to biodiversity. Biodiversity itself is known to reduce invasions and increase stability. Disturbances by ecosystem engineers affect the distribution, establishment, and abundance of species but this has been ignored in studies on diversity-invasibility relationships. Methodology/Principal Findings We determined natural plant invasion into 46 plots varying in the number of plant species (1, 4, and 16) and plant functional groups (1, 2, 3, and 4) for three years beginning two years after the establishment of the Jena Experiment. We sampled subplots where earthworms were artificially added and others where earthworm abundance was reduced. We also performed a seed-dummy experiment to investigate the role of earthworms as secondary seed dispersers along a plant diversity gradient. Horizontal dispersal and burial of seed dummies were significantly reduced in subplots where earthworms were reduced in abundance. Seed dispersal by earthworms decreased with increasing plant species richness and presence of grasses but increased in presence of small herbs. These results suggest that dense vegetation inhibits the surface activity of earthworms. Further, there was a positive relationship between the number of earthworms and the number and diversity of invasive plants. Hence, earthworms decreased the stability of grassland communities against plant invasion. Conclusions/Significance Invasibility decreased and stability increased with increasing plant diversity and, most remarkably, earthworms modulated the diversity-invasibility relationship. While the impacts of earthworms were unimportant in low diverse (low earthworm densities) and high diverse (high floral structural complexity) plant communities, earthworms decreased the stability of intermediate diverse plant communities against plant invasion. Overall, the results document that fundamental processes in plant communities like plant seed burial and invader establishment are modulated by soil fauna calling for closer cooperation between soil animal and plant ecologists.
Eisenhauer, Nico; Milcu, Alexandru; Sabais, Alexander C. W.; Scheu, Stefan
Significant progress has recently been made in our understanding of animal regenerative biology, spurred on by the use of a wider range of model organisms and an increasing ability to use genetic tools in traditional models of regeneration. This progress has begun to delineate differences and similarities in the regenerative capabilities and mechanisms among diverse animal species, and to address
Panagiotis A. Tsonis; Alejandro Sánchez Alvarado
B19 virus is a human virus belonging to the genus Erythrovirus. The genetic diversity among B19 virus isolates has been reported to be very low, with less than 2% nucleotide divergence in the whole genome sequence. We have previously reported the isolation of a human erythrovirus isolate, termed V9, whose sequence was markedly distinct (>11% nucleotide divergence) from that of
Annabelle Servant; Syria Laperche; Francis Lallemand; Valerie Marinho; Guillemette De Saint Maur; Jean Francois Meritet; Antoine Garbarg-Chenon
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
Genetic diversity of 33 Elymus caninus accessions was investigated using isozyme, RAPD, and microsatellite markers. The three assays differed in the amount of polymorphism detected. Microsatellites detected the highest polymorphism. Six microsatellite primer pairs generated a total of 74 polymorphic bands (alleles), with an average of 15.7 bands per primer pair. Three genetic similarity matrices were estimated based on band presence or absence. Genetic diversity trees (dendrograms) were derived from each marker technique, and compared using Mantel's test. The correlation coefficients were 0.204, 0.267, and 0.164 between isozyme and RAPD distance matrices, RAPD and microsatellite distance matrices, and between isozyme and microsatellite distance matrices, respectively. The three methodologies gave differing views of the amount of variation present but all showed a high level of genetic variation in E. caninus. The following points may be drawn from this study whether based on RAPD, microsatellite, or isozyme data: (i) The Icelandic populations are consistently revealed by the three dendrograms. The congruence of the discrimination of this accession group by RAPD, microsatellite, and isozyme markers suggests that geographic isolation strongly influenced the evolution of the populations; (ii) The degree of genetic variation within accessions was notably great; and (iii) The DNA-based markers will be the more useful ones in detecting genetic diversity in closely related accessions. In addition, a dendrogram, which took into account all fragments produced by isozymes, RAPDs, and microsatellites, reflected better the relationships than did dendrograms based on only one type of marker. PMID:10382290
Sun, G L; Díaz, O; Salomon, B; von Bothmer, R
Lagerstroemia (crape myrtle) are famous ornamental plants with large pyramidal racemes, long flower duration, and diverse colors. However, little is known about the genetic structure and diversity of germplasm in Lagerstroemia. We genotyped 81 L. indica cultivars, five other species of Lagerstroemia, and 10 interspecific hybrids using 30 simple sequence repeat markers; 275 alleles were generated with a mean of nine alleles per locus. The mean polymorphism information content value, a measure of gene diversity, was 0.63, with a range from 0.25 to 0.86. The mean observed heterozygosity (0.51) tended to be lower than the mean expected heterozygosity (0.67). The mean F-statistics (F(ST), F(IS), and F(IT)) were 0.05, 0.20, and 0.24, respectively, indicating a high level of genetic variation among cultivars. Clustering analysis based on genetic distance divided the 96 genotypes into three distinct groups, which corresponded with their genetic backgrounds and geographic regions. L. indica cultivars and the other five L. species were grouped into different sub-clusters. Chinese and North American cultivars were divided into different clusters. These data about the genetic relationship among cultivars demonstrated the potential value of L. indica cultivars and other Lagerstroemia species for widening the genetic basis of breeding programs for this ornamental flower. PMID:23079847
He, D; Liu, Y; Cai, M; Pan, H T; Zhang, Q X; Wang, X Y; Wang, X J
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
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.
Vallejo-Marin, M; Lye, G C
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
Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized—reproductively and genetically—worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.
Catania, Francesco; Wurmser, Francois; Potekhin, Alexey A.; Przybos, Ewa; Lynch, Michael
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.
Discusses facilitating opportunities for a grounded knowledge base, building culturally competent relationships, facilitating discussion of stereotyping, and forming collaborative alliances with culturally and ethnically diverse communities. Asserts that child welfare workers need to lay a foundation of excellence in these areas and presents child…
Woodroffe, Annette; Spencer, Mavis
A methodological approach to the identification of biodiversity indicators in commercial forest stands is illustrated by analysis of the relationships between syrphid (hoverflies) and carabid (ground beetles) community composition and diversity, and stand structure and field layer vegetation. Data were collected from 12 commercial forest sites encompassing a range of climatic conditions and different crop types (Scots pine, Sitka spruce,
J. W Humphrey; C Hawes; A. J Peace; R Ferris-Kaan; M. R Jukes
Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations. PMID:24963708
Buckland, Steeves; Cole, Nik C; Groombridge, Jim J; Küpper, Clemens; Burke, Terry; Dawson, Deborah A; Gallagher, Laura E; Harris, Stephen
Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.
Buckland, Steeves; Cole, Nik C.; Groombridge, Jim J.; Kupper, Clemens; Burke, Terry; Dawson, Deborah A.; Gallagher, Laura E.; Harris, Stephen
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
The cyst-forming protozoan parasite Neosporacaninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N. caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N. caninum, which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N. caninum-derived reference isolates from around the world and 96 N. caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N. caninum. Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N. caninum samples. Geographic sub-structuring was present in the country populations according to pairwise FST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N. caninum MLGs in cattle.
Regidor-Cerrillo, Javier; Diez-Fuertes, Francisco; Garcia-Culebras, Alicia; Moore, Dadin P.; Gonzalez-Warleta, Marta; Cuevas, Carmen; Schares, Gereon; Katzer, Frank; Pedraza-Diaz, Susana; Mezo, Mercedes; Ortega-Mora, Luis M.
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.
Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species’ range. In 136 effective samples from different individuals (range: 7–37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.
Higuchi, Shoko; Sakamaki, Tetsuya; Hart, John A.; Hart, Terese B.; Tokuyama, Nahoko; Reinartz, Gay E.; Guislain, Patrick; Dupain, Jef; Cobden, Amy K.; Mulavwa, Mbangi N.; Yangozene, Kumugo; Darroze, Serge; Devos, Celine; Furuichi, Takeshi
Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation. PMID:23544084
Kawamoto, Yoshi; Takemoto, Hiroyuki; Higuchi, Shoko; Sakamaki, Tetsuya; Hart, John A; Hart, Terese B; Tokuyama, Nahoko; Reinartz, Gay E; Guislain, Patrick; Dupain, Jef; Cobden, Amy K; Mulavwa, Mbangi N; Yangozene, Kumugo; Darroze, Serge; Devos, Céline; Furuichi, Takeshi
Mitochondrial DNA (mtDNA) D-loop sequences of 666 individuals (including 109 new individuals, 557 individuals retrieved from GenBank) from 33 Chinese domestic goat breeds throughout China were used to investigate their mtDNA variability and molecular phylogeography. The results showed that all goat breeds in this study proved to be extremely diverse, and the average haplotype diversity and nucleotide diversity were 0.990 ± 0.001 and 0.032 ± 0.001, respectively. The 666 sequences gave 326 different haplotypes. Phylogenetic analyses revealed that there were 4 mtDNA haplogroups identified in Chinese domestic goats, in which haplogroup A was predominant and widely distributed. Our finding was consistent with archaeological data and other genetic diversity studies. Amova analysis showed there was significant geographical structuring. Almost 84.31 % of genetic variation was included in the within-breed variance component and only 4.69 % was observed among the geographic distributions. This genetic diversity results further supported the previous view of multiple maternal origins of Chinese domestic goats, and the results on the phylogenetic relationship contributed to a better understanding of the history of goat domestication and modern production of domestic goats. PMID:24532161
Zhao, Yongju; Zhao, Runze; Zhao, Zhongquan; Xu, Huizhong; Zhao, Erhu; Zhang, Jiahua
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
Oenocarpus mapora is an Amazonian palm species commonly used by native populations for food and in folk medicine. We measured genetic variability, using RAPD markers, of material kept in a germplasm bank composed of accessions sampled from the Brazilian Amazon. These included 74 individuals from 23 accessions sampled from 9 localities in three States of the Brazilian Amazon. Jaccard genetic similarities were calculated based on 137 polymorphic bands, amplified by 15 primers. Dendrograms constructed based on the genetic similarities among individuals and sample localities demonstrated genetic separation of Acre State from the States of Amazonas and Pará. Two models in three hierarchical levels were considered for AMOVA: one considering the grouping of sampling sites in each state, and the other considering sampling sites in each subgroup formed by the dendrograms. The first model showed no significant genetic variation among states. On the other hand, genetic variation among subgroups was significant. In this model, the within-sample-site genetic diversity was 47.15%, which is considered to be low, since O. mapora is allogamous. By means of Bayesian analysis, the sample sites were clustered into five groups, and their distribution was similar to what we found in the dendrograms based on genetic similarity. PMID:23212338
Moura, E F; de Oliveira, M S P
Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host's phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes. PMID:24671440
Nakamura, Ginji; Kimura, Shigeko; Sako, Yoshihiko; Yoshida, Takashi
Honey bee (Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency (m e ) of this population of honey bee queens to be 13.6?±?6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ???7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e ?>?7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated. PMID:23728203
Tarpy, David R; Vanengelsdorp, Dennis; Pettis, Jeffrey S
Information on the genetic background of soybean [Glycine max (L.) Merr.] germplasm resistant to Soybean Cyst Nematode (SCN)\\u000a (Heterodera glycines Ichinohe) is essential for developing plant breeding strategies, however, pedigree information for SCN\\u000a resistant germplasm is not always available. Using restriction fragment length polymorphisms (RFLPs) to fingerprint different\\u000a soybean lines is a useful means of determining genetic relationships and identifying
J. Zhang; P. R. Arelli; D. A. Sleper; B. X. Qiu; M. R. Ellersieck
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
Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...
This study aimed to assess genetic diversity within and between nine Vietnamese local chicken breeds and two Chinese breeds included for comparison. Genotyping 29 microsatellites revealed high diversity of both Vietnamese and Chinese breeds. Cluster analysis using the STRUCTURE software suggested six clusters as the most likely grouping of the 11 breeds studied. These groups encompassed four homogeneous clusters, one formed by the two Chinese breeds and the other three representing a single breed each: the Mekong Delta breed Ac, the South Central Coast breed Choi, and the Red River Delta breed Dong Tao. The six remaining breeds formed two additional admixed clusters. PMID:20394606
Cuc, N T K; Simianer, H; Eding, H; Tieu, H V; Cuong, V C; Wollny, C B A; Groeneveld, L F; Weigend, S
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
Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F(2) individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01. PMID:21637582
Karakas, Ozge; Gurel, Filiz; Uncuoglu, Ahu Altinkut
Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii. PMID:19085060
Wang, Hui-Zhong; Wu, Zhen-Xing; Lu, Jiang-Jie; Shi, Nong-Nong; Zhao, Yan; Zhang, Zhi-Tao; Liu, Jun-Jun
Palestine has a wide range of agro-ecological concerns and hosts a large variety of plants. Grapes are part of the cultural heritage and provide an indispensable food ingredient. Local cultivars have been traditionally identified on the basis of morphological traits, geographical origin, or names of the vineyard owner; therefore, the occurrence of homonymy, synonymy, and misnaming significantly prevents their valorization. DNA profiling by 22 common SSR markers was used to characterize 43 putative cultivars grown mainly for local table grape consumption at the southern highland regions of West-Bank, to further evaluate genetic diversity and relationships of the population. Consistent matching of SSR markers with grapevines cultivated in neighboring countries or maintained in European germplasm collections was found for 8 of the 21 different non-redundant genotypes discovered, suggesting possible synonyms as well as the occurrence of breeding selections formerly developed in the USA. Genetic relationships inferred from SSR markers clearly assigned Palestinian cultivars to the Proles orientalis subpr. Antasiatica ancestral population, and they even remarked the connection between local resources and cultivars generated from international table grape breeding. This study supports the value of collection and conservation of vines endemic to a region of immense historical importance for viticulture. PMID:24469973
Basheer-Salimia, Rezq; Lorenzi, Silvia; Batarseh, Fadi; Moreno-Sanz, Paula; Emanuelli, Francesco; Grando, M Stella
Genetic diversity study of Koompassia malaccensis based on 19 populations from 18 forest reserves located throughout Peninsular Malaysia was reported. The average number of samples analyzed per population was 24. Genetic diversity assessment was based on six polymorphic microsatellites. Overall, all the populations showed high levels of genetic diversity. The allelic richness ranged from 6.0 (Pekan) to 9.3 (Lenggur) whereas
C. T. Lee; S. L. Lee; Q. Z. Faridah; S. S. Siraj; K. K. S. Ng; M. Norwati
The basking shark (Cetorhinus maximus) is found in temperate waters throughout the world's oceans, and has been subjected to extensive exploitation in some regions. However, little is known about its current abundance and genetic status. Here, we investigate the diversity of the mitochondrial DNA control region among samples from the western North Atlantic, eastern North Atlantic, Mediterranean Sea, Indian Ocean and western Pacific. We find just six haplotypes defined by five variable sites, a comparatively low genetic diversity of ?=0.0013 and no significant differentiation between ocean basins. We provide evidence for a bottleneck event within the Holocene, estimate an effective population size (Ne) that is low for a globally distributed species, and discuss the implications.
Rus Hoelzel, A; Shivji, Mahmood S; Magnussen, Jennifer; Francis, Malcolm P
In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were collected nine months apart, demonstrating long-term virus circulation. The bat colony was estimated to be over 100,000 animals using mark and re-capture methods, predicting the presence of over 5,000 virus-infected bats. The genetically diverse virus genome sequences from bats and miners closely matched. These data indicate common Egyptian fruit bats can represent a major natural reservoir and source of Marburg virus with potential for spillover into humans.
Towner, Jonathan S.; Amman, Brian R.; Sealy, Tara K.; Carroll, Serena A. Reeder; Comer, James A.; Kemp, Alan; Swanepoel, Robert; Paddock, Christopher D.; Balinandi, Stephen; Khristova, Marina L.; Formenty, Pierre B. H.; Albarino, Cesar G.; Miller, David M.; Reed, Zachary D.; Kayiwa, John T.; Mills, James N.; Cannon, Deborah L.; Greer, Patricia W.; Byaruhanga, Emmanuel; Farnon, Eileen C.; Atimnedi, Patrick; Okware, Samuel; Katongole-Mbidde, Edward; Downing, Robert; Tappero, Jordan W.; Zaki, Sherif R.; Ksiazek, Thomas G.; Nichol, Stuart T.; Rollin, Pierre E.
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
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
In July and September 2007, miners working in Kitaka Cave, Uganda, were diagnosed with Marburg hemorrhagic fever. The likely source of infection in the cave was Egyptian fruit bats (Rousettus aegyptiacus) based on detection of Marburg virus RNA in 31\\/611 (5.1%) bats, virus-specific antibody in bat sera, and isolation of genetically diverse virus from bat tissues. The virus isolates were
Jonathan S. Towner; Brian R. Amman; Tara K. Sealy; Serena A. Reeder Carroll; James A. Comer; Alan Kemp; Robert Swanepoel; Christopher D. Paddock; Stephen Balinandi; Marina L. Khristova; Pierre B. H. Formenty; Cesar G. Albarino; David M. Miller; Zachary D. Reed; John T. Kayiwa; James N. Mills; Deborah L. Cannon; Patricia W. Greer; Emmanuel Byaruhanga; Eileen C. Farnon; Patrick Atimnedi; Samuel Okware; Edward Katongole-Mbidde; Robert Downing; Jordan W. Tappero; Sherif R. Zaki; Thomas G. Ksiazek; Stuart T. Nichol; Pierre E. Rollin
Genetic diversity was estimated in 37 neem accessions from different eco-geographic regions of India and four exotic lines\\u000a from Thailand using AFLP markers. Seven AFLP selective primer combinations generated a total of 422 amplification products.\\u000a The average number of scorable fragments was 60 per experiment, and a high degree (69.8%) of polymorphism was obtained per\\u000a assay with values ranging from
A. Singh; M. S. Negi; J. Rajagopal; S. Bhatia; U. K. Tomar; P. S. Srivastava; M. Lakshmikumaran
Intra-specific diversity in Liularia vellerea growing in the northwestern to central Yunnan province of China was studied by chemical and genetic approaches. Samples collected in the Jianchuan, Lijiang, and Zhongdian areas contained 6,15-dioxygenated furanoeremophilanes as their major components (type A); whereas samples from the Luguhu area accumulated 1,6-dioxygenated furanoeremophilanes (type B); a sample from near Kunming, however, contained 6,15-dioxygenated eremophilanolides
Motoo Tori; Hiromi Nakamizo; Kanako Mihara; Masahiko Sato; Yasuko Okamoto; Katsuyuki Nakashima; Masami Tanaka; Yoshinori Saito; Masakazu Sono; Xun Gong; Yuemao Shen; Ryo Hanai; Chiaki Kuroda
Salvia miltiorrhiza Bge is a traditional Chinese medicinal herb used as an important drug to cure cardiovascular diseases. In this work, inter simple sequence repeats (ISSR) and sequence related amplified polymorphism (SRAP) markers, were applied to assess the level and pattern of genetic diversity in five important cultivated populations of S. miltiorrhiza. Among these populations, 120 bands were amplified by 5 ISSR primers, of which all were polymorphic, and 110 polymorphic bands (90.16%) were observed in 122 bands amplified by 6 SRAP primers. A high levels of genetic diversity at the species level was detected with Hs = 0.1951, 0.1927 respectively. Analysis of molecular variance revealed that a greater proportion of total genetic variation existed within populations (86.64 and 84.83% respectively) rather than among populations (13.36 and 15.17% respectively). Cluster analysis divided the five populations into two groups. The genetic relationships among populations have low correlation with their geographical distribution (Mantel test; r = 0.4870 and 0.5740 respectively). The study indicated that both ISSR and SRAP markers were effective and reliable for assessing the degree of genetic variation of S. miltiorrhiza. Our results suggested that random collecting, preserving and planting seeds without deliberate selection might be an efficient way to conserve genetic resources of medicinal plants. Their effective use was also discussed on the further breeding. PMID:19844793
Song, Zhenqiao; Li, Xingfeng; Wang, Honggang; Wang, Jianhua
Eggplant (Solanum melongena), a vegetable that is cultivated worldwide, is of considerable importance to agriculture in China. We analyzed the diversity of this plant using inter-simple sequence repeat (ISSR) and RAPD procedures to subdivide 143 Chinese-cultivated eggplants based on coefficient of parentage, genetic diversity index (GDI) and canonical discriminant analysis. ISSR markers were more effective than RAPD markers for detecting genetic diversity, which ranged from 0.10-0.51, slightly lower than what is known from other crops. Our ISSR/RAPD data provide molecular evidence that coincides with morphological-based classification into three varieties and further subdivision into eight groups, except for two groups. Intensive use of elite parents and extensive crossing within groups have resulted in increased coefficient of parentage and proportional contribution but decreased GDI during the past decades. The mean coefficient of parentage and proportional contribution increased from 0.05 to 0.10% and from 3.22 to 6.46% during 1980-1991 and 1992-2003, respectively. The GDI of landraces was 0.21, higher than the 0.09 and 0.08 calculated for the hybrid cultivars released during the two periods. The recent introduction of alien genotypes into eggplant breeding programs may broaden the genetic base. PMID:21710466
Ali, Z; Xu, Z L; Zhang, D Y; He, X L; Bahadur, S; Yi, J X
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.
Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy-Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity. PMID:23269618
Li, Di Yan; Xu, Huai Liang; Trask, Jessica Satkoski; Zhu, Qing; Cheng, An Chun; Smith, David Glenn; George, Debbie; Zhang, Long
We evaluated mitochondrial cytochrome oxidase I genetic diversity of two barnacle species (Eochionelasmus ohtai manusensis, Vulcanolepas cf. parensis) at three sites in Manus Basin (Solwara 1, South Su, Solwara 8). There was no evidence for within-site or between-site genetic differentiation for either species. While E. ohtai manusensis showed limited genetic variation, V. cf. parensis showed greater variation, with sequences distributed between two divergent groups. Assuming the cytochrome oxidase I gene is not under selection, significantly negative Tajima's D in E. ohtai manusensis is consistent with a recent population expansion due to a bottleneck or founder effect, whereas V. cf. parensis (combined groups) did not depart from a stable effective population size. Considering the groups separately, V. cf. parensis Group 1 (but not Group 2) showed a negative Tajima's D, indicating these groups may have encountered different historical demographic conditions. Data reported here are part of a baseline study against which recovery of genetic diversity following mineral extraction at Solwara 1 can be measured.
Plouviez, Sophie; Schultz, Thomas F.; McGinnis, Gwendolyn; Minshall, Halle; Rudder, Meghan; Van Dover, Cindy L.
BACKGROUND: Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored. RESULTS: To analyze an unbiased sample of genetic diversity in India and to investigate human migration
Jinchuan Xing; W Scott Watkins; Ya Hu; Chad D Huff; Aniko Sabo; Donna M Muzny; Michael J Bamshad; Richard A Gibbs; Lynn B Jorde; Fuli Yu
Studies on the effects of biodiversity on ecosystem functioning have generally revealed a positive asymptotic relationship between biodiversity and single functions, suggesting species redundancy with respect to these functions. However, most research was performed on specific processes and did not consider ecosystem 'multifunctionality'. There is also little information on the relationship between genetic and functional diversity. To analyze this relationship, we performed a microcosm experiment on a complex lake assemblage of decomposers, in the presence of the green alga Scenedesmus obliquus, which acted as carbon source for decomposers. By manipulating nutrient enrichment and the N : P input ratio, we observed that the structures of particle-associated and free bacterial assemblages were highly predictable in response to stoichiometric constraints. For a given treatment, the taxonomic compositions of free and particle-associated bacterial communities appeared close to each other only when phosphorus was not depleted. A coinertia analysis revealed a clear coupling between the genetic diversity of the microbial community, assessed using PCR-denatured gradient gel electrophoresis, and its potential functional diversity, studied with Biolog Ecoplates. This suggests that an ecologically relevant fraction of bacterial communities is characterized by lower level of redundancy than frequently thought, highlighting the necessity of exploring further the role of biodiversity in multifunctionality within ecosystems. PMID:18811649
Leflaive, Joséphine; Danger, Michael; Lacroix, Gérard; Lyautey, Emilie; Oumarou, Catherine; Ten-Hage, Loïc
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
We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants.
Song, Jeong Young; Seo, Mun Won; Kim, Sun Ick; Nam, Myeong Hyeon; Lim, Hyoun Sub
We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants. PMID:25071387
Song, Jeong Young; Seo, Mun Won; Kim, Sun Ick; Nam, Myeong Hyeon; Lim, Hyoun Sub; Kim, Hong Gi
In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...
Background Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds. Methods For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds’ genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach. Results Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds’ genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank. Conclusions A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.
Genetic diversity and relationships were assessed in 28 accessions of Musa acuminata (AA) Colla and Musa balbisiana (BB) Colla, and some of their natural hybrids, using the amplified fragment length polymorphisms (AFLP) technique. Fifteen AFLP +3 primer pairs produced 527 polymorphic bands among the accessions. Neighbor-joining and principal co-ordinate (PCO) analyses using Jaccard's similarity coefficient produced four major clusters that
G. Ude; M. Pillay; D. Nwakanma; A. Tenkouano
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.
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
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
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
The aim of the present study was to investigate the genetic diversity of Gallibacterium isolates recovered from lesions in turkeys. Gallibacterium has been isolated from various bird species including turkeys, but no large investigations have yet been made to characterize isolates from turkeys genetically. We therefore genotyped 53 Gallibacterium isolates obtained from turkeys between 1998 and 2004. Fifty isolates originated from 29 different flocks in California and the remaining three came from three German turkey flocks. All were recovered from birds with lesions, mainly in the upper respiratory tract. Five chicken isolates from California and five Gallibacterium reference strains were also included. Amplified fragment length polymorphism analysis demonstrated substantial genetic diversity among the Gallibacterium isolates. However, we also demonstrated that some Gallibacterium clones were present in consecutive rotations at the same farm during the entire 6-year observation period and were present in different flocks from different farms. Similarly, the same clone was identified from two of the three German flocks. Further investigation of the spread of Gallibacterium between turkey flocks, including infections acquired from chickens or wild birds, should be carried out. PMID:17497336
Bojesen, A M; Shivaprasad, H L
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.
There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.
Maccari, Marta; Amat, Francisco; Gomez, Africa
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
Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively. The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of 153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift, sampling of loci and unknown relationships among supposedly unrelated ancestors. PMID:11294614
Davierwala, A P; Chowdari, K V; Kumar, S; Reddy, A P; Ranjekar, P K; Gupta, V S
The success of many strategies for finding genetic variants that underlie complex traits depends on how genetic variation is distributed among human populations. This realization has intensified the investigation of genetic differences among groups, which are often defined by commonly used racial labels. Some scientists argue that race is an adequate proxy of ancestry, whereas others claim that race belies
Stephen Wooding; Benjamin A. Salisbury; J. Claiborne Stephens; Michael Bamshad
Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.
Rueppell, Olav; Meier, Stephen; Deutsch, Roland
The spontaneous generation of distinct phenotypes within a clonal population of cells allows for both bet-hedging at the population level and the division of labor among subpopulations. This is emerging as an important theme in bacterial pathogenesis, because bacterial pathogens exhibit phenotypic heterogeneity with respect to characteristics that impact virulence. The phenomenon of persister cells and models of Salmonella enterica serovar Typhimurium (S. Typhimurium) pathogenesis illustrate the importance of non-genetic diversity in the disease process. Such heterogeneity can arise from specific genetic architectures amplifying stochastic fluctuations in factors affecting gene expression, and this also drives variation in eukaryotic cells. Thus reproducible variation in both host and pathogen processes affects the outcome of infection. PMID:22889945
Stewart, Mary K; Cookson, Brad T
The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.
Jobling, Mark A.
Academic-industry research relationships (AIRRS) have become widely accepted and increasingly common in the life sciences. Using nationwide surveys from the United States, we found significant differences between the AIRRs of genetics firms and faculty and those of other firms and faculty. Significantly more genetics than non-genetics firms funded AIRRs, and genetics firms' AIRRs were larger and longer. Genetics faculty with AIRRs were significantly more likely than non-genetics faculty to report that patents, licenses, new companies and trade secrets had resulted from their university research; and that they had refused to share research results of biomaterials with colleagues. PMID:9140405
Blumenthal, D; Causino, N; Campbell, E G
Species endangerment often derives from the "endangerment" of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during 1998-1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity. PMID:16944294
Multiple mating by social insect queens increases the genetic diversity among colony members, thereby reducing intracolony relatedness and lowering the potential inclusive fitness gains of altruistic workers. Increased genetic diversity may be adaptive, however, by reducing the prevalence of disease within a nest. Honeybees, whose queens have the highest levels of multiple mating among social insects, were investigated to determine whether genetic variation helps to prevent chronic infections. I instrumentally inseminated honeybee queens with semen that was either genetically similar (from one male) or genetically diverse (from multiple males), and then inoculated their colonies with spores of Ascosphaera apis, a fungal pathogen that kills developing brood. I show that genetically diverse colonies had a lower variance in disease prevalence than genetically similar colonies, which suggests that genetic diversity may benefit colonies by preventing severe infections.
Tarpy, David R
Arctomecon humilis is a critically endangered species endemic to the Moenkopi shale of Washington County, Utah. Recovery plans for the species would be improved by an understanding of genetic diversity and gene flow among its remaining populations. Ten variable isozyme loci were used to calculate genetic diversity statistics for study populations. Westerly populations possessed higher levels of genetic variability than
Loreen Allphin; Michael D. Windham; Kimball T. Harper
My long-term goals are focused on deciphering the role genetic diversity plays in regulating the formation and decline of plankton-rich layers (PRLs). I plan to examine: (1) the mechanistic roles that genetic diversity and genetic composition play in the ...
T. A. Rynearson
My long-term goals are focused on deciphering the role genetic diversity plays in regulating the formation and decline of plankton-rich layers (PRLs). I plan to examine (1) the mechanistic roles that genetic diversity and genetic composition play in the e...
T. A. Rynearson
Conservation strategies for whole communities at the landscape scale have rarely been able to take into account genetic diversity because of the number of species involved. However, if species can be grouped together by geographic distribution of genetic diversity and patterns of relatedness, then landscape and genetic conservation might be more effectively combined to cope with problems of fragmentation. We
Bo-Chi G. Lai; Andrew S. Pullin
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.
This article uses stochastic simulations with a compartmental epidemic model to quantify the impact of genetic diversity within animal populations on the transmission of infectious disease. Genetic diversity is defined by the number of distinct genotypes in the population conferring resistance to microparasitic (e.g., viral or bacterial) infections. Scenarios include homogeneous populations and populations composed of few (finite-locus model) or many (infinitesimal model) genotypes. Genetic heterogeneity has no impact upon the expected value of the basic reproductive ratio (the primary description of the transmission of infection) but affects the variability of this parameter. Consequently, increasing genetic heterogeneity is associated with an increased probability of minor epidemics and decreased probabilities of both major (catastrophic) epidemics and no epidemics. Additionally, heterogeneity per se is associated with a breakdown in the expected relationship between the basic reproductive ratio and epidemic severity, which has been developed for homogeneous populations, with increasing heterogeneity generally resulting in fewer infected animals than expected. Furthermore, increased heterogeneity is associated with decreased disease-dependent mortality in major epidemics and a complex trend toward decreased duration of these epidemics. In summary, more heterogeneous populations are not expected to suffer fewer epidemics on average, but are less likely to suffer catastrophic epidemics.
Springbett, A J; MacKenzie, K; Woolliams, J A; Bishop, S C
Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history and geographical divisions of native breeding regions of indigenous cattle. Divergence estimates between Icelandic cattle and indigenous breeds suggested a separation time of more than 1,000 years between Icelandic cattle and Norwegian native breeds, a finding consistent with historical evidence. PMID:11218082
Kantanen, J; Olsaker, I; Holm, L E; Lien, S; Vilkki, J; Brusgaard, K; Eythorsdottir, E; Danell, B; Adalsteinsson, S
The recent development of microsatellite markers for tobacco, Nicotiana tabacum L., may be valuable for genetic studies within the genus Nicotiana. The first objective was to evaluate transferability of 100 N. tabacum microsatellite primer combinations to 5 diploid species closely related to tobacco. The number of primer combinations that amplified scorable bands in these species ranged from 42 to 56. Additional objectives were to assess levels of genetic diversity amongst available accessions of diploid relatives closely related to tobacco (species of sections Sylvestres and Tomentosae), and to evaluate the efficacy of microsatellite markers for establishing species relationships in comparison with existing phylogenetic reconstructions. A subset of 46 primer combinations was therefore used to genotype 3 synthetic tobaccos and an expanded collection of 51 Nicotiana accessions representing 15 species. The average genetic similarity for 7 diverse accessions of tobacco was greater than the average similarity for N. otophora accessions, but lower than the average genetic similarities for N. sylvestris, N. tomentosa, N. kawakamii, and N. tomentosiformis accessions. A microsatellite-based phylogenetic tree was largely congruent with taxonomic representations based on morphological, cytological, and molecular observations. Results will be useful for selection of parents for creation of diploid mapping populations and for germplasm introgression activities. PMID:18650945
Moon, H S; Nicholson, J S; Lewis, R S
Three molecular marker systems, Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeats (ISSR) and Sequence-Related Amplified Polymorphism (SRAP) were employed to investigate the genetic structure and diversity among the 14 natural populations of Butea monosperma collected from different geographical regions of India. Detected by 17 RAPD, 15 ISSR and 11 SRAP primer combinations, the proportions of polymorphic bands were 84.2 %, 77.2 % and 91.9 %, respectively, and the mean Nei's genetic distances among the populations were 0.13, 0.10 and 0.13, respectively. Partitioning of genetic variability by Analysis of molecular variance (AMOVA) revealed that the high genetic diversity was distributed within the populations. AMOVA also revealed that the coefficient of gene differentiation among populations based on FST was very high irrespective of markers used. The overall gene flow among populations (Nm) was very low. Cophenetic correlation coefficients of Nei's distance values and clustering pattern by Mental test were statistically significant for all three marker systems used but poor fit for ISSR data than for RAPD, SRAP and combined data set of all three markers. For all markers, a high similarity in dendrogram topologies was obtained, although some differences were observed with ISSR. The dendrogram obtained by RAPD, SRAP and combined data set of all three markers reflect relationship of most of the populations according to their geographic distribution. PMID:24431507
Vashishtha, Amit; Jehan, Tabassum; Lakhanpaul, Suman
Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.
Aranguren-Mendez, Jose; Jordana, Jordi; Gomez, Mariano
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.
To assess the genetic diversity in Cryptosporidium parvum, we have sequenced the small subunit (SSU) rRNA gene of seven Cryptosporidium spp., various isolates of C. parvum from eight hosts, and a Cryptosporidium isolate from a desert monitor. Phylogenetic analysis of the SSU rRNA sequences confirmed the multispecies nature of the genus Cryptosporidium, with at least four distinct species (C. parvum, C. baileyi, C. muris, and C. serpentis). Other species previously defined by biologic characteristics, including C. wrairi, C. meleagridis, and C. felis, and the desert monitor isolate, clustered together or within C. parvum. Extensive genetic diversities were present among C. parvum isolates from humans, calves, pigs, dogs, mice, ferrets, marsupials, and a monkey. In general, specific genotypes were associated with specific host species. A PCR-restriction fragment length polymorphism technique previously developed by us could differentiate most Cryptosporidium spp. and C. parvum genotypes, but sequence analysis of the PCR product was needed to differentiate C. wrairi and C. meleagridis from some of the C. parvum genotypes. These results indicate a need for revision in the taxonomy and assessment of the zoonotic potential of some animal C. parvum isolates. PMID:10427023
Xiao, L; Morgan, U M; Limor, J; Escalante, A; Arrowood, M; Shulaw, W; Thompson, R C; Fayer, R; Lal, A A
Blastocystis sp. is a common intestinal parasite found in humans and animals. The possibility of zoonotic transmission to humans from livestock especially goats led us to investigate the genetic diversity of caprine Blastocystis sp. obtained from five different farms in Peninsular Malaysia. Moreover, there is a lack of information on the prevalence as well as genetic diversity of Blastocystis sp. in goat worldwide. Results showed that 73/236 (30.9 %) of the goats were found to be positive for Blastocystis infection. The most predominant Blastocystis sp. subtype was ST1 (60.3 %) followed by ST7 (41.1 %), ST6 (41.1 %), and ST3 (11.0 %) when amplified by PCR using sequenced-tagged site (STS) primers. Four farms had goats infected only with ST1 whereas the fifth showed mixed infections with multiple STs. The proximity of the fifth farm to human dwellings, nearby domesticated animals and grass land as opposed to a sterile captive environment in the first four farms may account for the multiple STs seen in the fifth farm. Since ST1, ST3, ST6 and ST 7 were previously reported in human infection worldwide in particular Malaysia, the potential of the zoonotic transmission of blastocystosis should not be disregarded. The implications of different farm management systems on the distribution of Blastocystis sp. STs are discussed. PMID:22961236
Tan, Tian Chye; Tan, Peng Chiang; Sharma, Reuben; Sugnaseelan, Sumita; Suresh, Kumar Govind
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.
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.
Avian paramyxoviruses (APMVs) belong to the genus Avulavirus in the family Paramyxoviridae and include at least nine serotypes, APMV-1 to -9, as well as two additional provisional serotypes. Newcastle disease virus (NDV), which comprises APMV-1, is the most extensively studied APMV because it is an important poultry pathogen. A moderate level of antigenic and genetic diversity is recognized for APMV-1 isolates, but our knowledge of the antigenic and genetic diversity of the other APMV serotypes is limited. APMV-4 is frequently isolated from waterfowl around the world. To date complete genome sequences of APMV-4 are available for only strains, which were isolated from ducks in Hong Kong, Korea and Belgium over a period of 37 years. We have carried out genome sequencing from the nucleocapsid (N) gene-end signal to the polymerase (L) gene-start signal of five APMV-4 strains recently isolated from Italy. Each of the eight APMV-4 strains has the same F protein cleavage site, DIQPR?F. They also share a high level of nucleotide and amino acid sequence identity: for example, the F and HN glycoproteins have greater than 97% sequence identity between the various strains. Thus, comparison of these eight strains of APMV-4 did not provide evidence of substantial diversity, in contrast to similar studies with APMV-2, -3, and -6, in which the F and HN glycoproteins exhibited up to 20-30% amino acid sequence variation within a subgroup. Reciprocal cross-HI assay using post infection chicken sera also failed to detect significant antigenic variation among the available APMV-4 strains.
Nayak, Baibaswata; Nayak, Shreeraj; Paldurai, Anandan; Kumar, Sachin; De Nardi, Roberta; Terregino, Calogero; Collins, Peter L; Samal, Siba K
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
Standard methods used to estimate HIV-1 population diversity are often resource intensive (e.g., single genome amplification, clonal amplification and pyrosequencing) and not well suited for large study cohorts. Additional approaches are needed to address the relationships between intraindividual HIV-1 genetic diversity and 2 disease. With a small cohort of individuals, we validated three methods for measuring diversity: Shannon entropy and average pairwise distance (APD) using single genome sequences, and counts of mixed bases (i.e. ambiguous nucleotides) from population based sequences. In a large cohort, we then used the mixed base approach to determine associations between measure HIV-1 diversity and HIV associated disease. Normalized counts of mixed bases correlated with Shannon Entropy at both the nucleotide (rho=0.72, p=0.002) and amino acid level (rho=0.59, p=0.015), and APD (rho=0.75, p=0.001). Among participants who underwent neuropsychological and clinical assessments (n=187), increased HIV-1 population diversity was associated with both a diagnosis of AIDS and neuropsychological impairment. PMID:22999095
Hightower, George K; Wong, Joseph K; Letendre, Scott L; Umlauf, Anya A; Ellis, Ronald J; Ignacio, Caroline C; Heaton, Robert K; Collier, Ann C; Marra, Christina M; Clifford, David B; Gelman, Benjamin B; McArthur, Justin C; Morgello, Susan; Simpson, David M; McCutchan, J A; Grant, Igor; Little, Susan J; Richman, Douglas D; Kosakovsky Pond, Sergei L; Smith, Davey M
Cereal species of the grass tribe Triticeae are economically important and provide staple food for large parts of the human\\u000a population. The Fertile Crescent of Southwest Asia harbors high genetic and morphological diversity of these species. In this\\u000a study, we analyzed genetic diversity and phylogenetic relationships among D genome-bearing species of the wheat relatives of the genus Aegilops from Iran
Firouzeh Bordbar; Mohammad Reza Rahiminejad; Hojjatollah Saeidi; Frank R. Blattner
The genus Ostreopsis is an important component of benthic and epiphytic dinoflagellate assemblages in coral reefs and seaweed beds of Malaysia. Members of the species may produce toxins that contribute to ciguatera fish poisoning. In this study, two species have been isolated and cultured, Ostreopsis ovata and Ostreopsis lenticularis. Analyses of the 5.8S subunit and internal transcribed spacer regions ITS1 and ITS2 of the ribosomal RNA gene sequences of these two species showed that they are separate species, consistent with morphological designations. The nucleotide sequences of the 5.8S subunit and ITS1 and ITS2 regions of the rRNA gene were also used to evaluate the interpopulation and intrapopulation genetic diversity of O. ovata found in Malaysian waters. Results showed a low level of sequence divergence within populations. At the interpopulation level, the rRNA gene sequence distinguished two groups of genetically distinct strains, representative of a Malacca Straits group (isolates from Port Dickson) and a South China Sea group (isolates from Pulau Redang and Kota Kinabalu). Part of the sequences in the ITS regions may be useful in the design of oligonucleotide probes specific for each group. Results from this study show that the ITS regions can be used as genetic markers for taxonomic, biogeographic, and fine-scale population studies of this species. PMID:14961362
Pin, L C; Teen, L P; Ahmad, A; Usup, G
Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene-expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene-expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3?months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. PMID:24399611
Harbst, Katja; Lauss, Martin; Cirenajwis, Helena; Winter, Christof; Howlin, Jillian; Törngren, Therese; Kvist, Anders; Nodin, Björn; Olsson, Eleonor; Häkkinen, Jari; Jirström, Karin; Staaf, Johan; Lundgren, Lotta; Olsson, Håkan; Ingvar, Christian; Gruvberger-Saal, Sofia K; Saal, Lao H; Jönsson, Göran
Seven species (eight populations) of sentinel crabs (genus Macrophthalmus) from the Japan coast and Uca vocans and Ocypode ceratophthalma, were examined electrophoretically for genetic variations in 13 enzymatic and one non-enzymatic protein comprising 17 loci. Most species were highly differentiated from each other (Nei's genetic distance, 0.29-1.63). The least genetic distance was found between M. japonicus and M. banzai, the genetic distinctiveness of the two taxa being supported by three divergent loci with no common allele. The genetic relationships among Macrophthalmus species differed greatly from those inferred from morphological features, with a UPGMA tree suggesting that the sub-genus Macrophthalmus is polyphyletic. PMID:11470446
Horii, T; Kitaura, J; Wada, K; Nishida, M
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 >145000 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. PMID:23249956
Esko, Tõnu; Mezzavilla, Massimo; Nelis, Mari; Borel, Christelle; Debniak, Tadeusz; Jakkula, Eveliina; Julia, Antonio; Karachanak, Sena; Khrunin, Andrey; Kisfali, Peter; Krulisova, Veronika; Aušrelé Ku?inskiené, Zita; Rehnström, Karola; Traglia, Michela; Nikitina-Zake, Liene; Zimprich, Fritz; Antonarakis, Stylianos E; Estivill, Xavier; Glava?, Damjan; Gut, Ivo; Klovins, Janis; Krawczak, Michael; Ku?inskas, Vaidutis; Lathrop, Mark; Macek, Milan; Marsal, Sara; Meitinger, Thomas; Melegh, Béla; 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
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
Recent research indicates that low genetic variation in individuals can increase susceptibility to parasite infection, yet evidence from natural invertebrate populations remains scarce. Here, we studied the relationship between genetic heterozygosity, measured as AFLP-based inbreeding coefficient fAFLP , and gregarine parasite burden from eleven damselfly, Calopteryx splendens, populations. We found that in the studied populations, 5-92% of males were parasitized by endoparasitic gregarines (Apicomplexa: Actinocephalidae). Number of parasites ranged from none to 47 parasites per male, and parasites were highly aggregated in a few hosts. Mean individual fAFLP did not differ between populations. Moreover, we found a positive association between individual's inbreeding coefficient and parasite burden. In other words, the more homozygous the individual, the more parasites it harbours. Thus, parasites are likely to pose strong selection pressure against inbreeding and homozygosity. Our results support the heterozygosity-fitness correlation hypothesis, which suggests the importance of heterozygosity for an individual's pathogen resistance. PMID:23865399
Kaunisto, K M; Viitaniemi, H M; Leder, E H; Suhonen, J
India possesses a total buffalo population of 105 million out of which 26.1% inhabit Uttar Pradesh. The buffalo of Uttar Pradesh are described as nondescript or local buffaloes. Currently, there is no report about the genetic diversity, phylogenetic relationship and matrilineal genetic structure of these buffaloes. To determine the origin and genetic diversity of UP buffaloes, we sequenced and analysed the mitochondrial DNA D-loop sequences in 259 samples from entire Uttar Pradesh. One hundred nine haplotypes were identified in UP buffaloes that were defined by 96 polymorphic sites. We implemented neutrality tests to assess signatures of recent historical demographic events like Tajima’s D test and Fu’s Fs test. The phylogenetic studies revealed that there was no geographic differentiation and UP buffaloes had a single maternal lineage while buffaloes of Eastern UP were distinctive from rest of the UP buffaloes.
Joshi, Jyoti; Salar, R. K.; Banerjee, Priyanka; S, Upasna; Tantia, M. S.; Vijh, R. K.
There is increasing molecular and antigenic evidence that Pneumocystis carinii organisms isolated from humans, ferrets, and rats are different species. In contrast, little is known about the extent of genetic diversity among P. carinii strains found within a single mammalian species. In the present study, electrophoretic karyotypes were obtained from P. carinii prepared from 10 chronically immunosuppressed rat colonies to investigate diversity at the chromosomal level. Most organism preparations produced patterns with 13 to 15 bands, but as many as 24 bands were observed in a few preparations. All bands separated between 700 and 300 kbp. Four distinct karyotype forms emerged from among the 13- to 15-band karyotypes of the 10 colonies sampled. Form 1 was shared by five rat strains from two vendors; form 2 was shared by two rat strains from the same vendor; and forms 3 and 4 were unique to their vendor colonies. Within a given rat colony, most rats harbored the same P. carinii karyotype. A survey of selected rat colonies showed that the karyotype within a vendor colony could remain stable over a period of 2 to 3 years. Hybridization of the blotted karyotypes with a repetitive DNA element isolated from rat-derived P. carinii and with single-copy gene probes showed that every chromosome in the karyotypes contained some repetitive DNA, and there was a general size concordance among the chromosomes carrying the unique gene loci. Differences in gene sequences, electrophoretic karyotypes, and hybridization profiles suggested that the immunosuppressed rats were infected by genetically distinct P. carinii strains. A provisional system of nomenclature for P. carinii that will permit differentiation of P. carinii organisms from the same mammalian host is discussed. These data show that all rats were not infected by a single type of P. carinii, that pulsed-field gradient electrophoresis can detect sufficient genetic diversity among the organism preparations to allow for characterization of the organisms, and that the genome of the organism within the rat host is relatively stable over time. Images
Cushion, M T; Kaselis, M; Stringer, S L; Stringer, J R
Japanese goshawk was classified as a vulnerable species in the Red Data Book. There have been possibilities of a decrease\\u000a of genetic diversity accompanied by habitat loss and genetic pollution due to hybridization with escaping imported goshawks.\\u000a In this paper, genetic diversity, gene flow and conservation of Northern Goshawk (Accipiter gentilis) in Japan are discussed and compared with that in
Yoshihide Takaki; Takayuki Kawahara; Hisashi Kitamura; Ko-ichi Endo; Takuma Kudo
The shape of the productivity–diversity relationship (PDR) for marine phytoplankton has been suggested to be unimodal, that is, diversity peaking at intermediate levels of productivity. However, there are few observations and there has been little attempt to understand the mechanisms that would lead to such a shape for planktonic organisms. Here we use a marine ecosystem model together with the community assembly theory to explain the shape of the unimodal PDR we obtain at the global scale. The positive slope from low to intermediate productivity is due to grazer control with selective feeding, which leads to the predator-mediated coexistence of prey. The negative slope at high productivity is due to seasonal blooms of opportunist species that occur before they are regulated by grazers. The negative side is only unveiled when the temporal scale of the observation captures the transient dynamics, which are especially relevant at highly seasonal latitudes. Thus selective predation explains the positive side while transient competitive exclusion explains the negative side of the unimodal PDR curve. The phytoplankton community composition of the positive and negative sides is mostly dominated by slow-growing nutrient specialists and fast-growing nutrient opportunist species, respectively.
Vallina, S. M.; Follows, M. J.; Dutkiewicz, S.; Montoya, J. M.; Cermeno, P.; Loreau, M.
The shape of the productivity-diversity relationship (PDR) for marine phytoplankton has been suggested to be unimodal, that is, diversity peaking at intermediate levels of productivity. However, there are few observations and there has been little attempt to understand the mechanisms that would lead to such a shape for planktonic organisms. Here we use a marine ecosystem model together with the community assembly theory to explain the shape of the unimodal PDR we obtain at the global scale. The positive slope from low to intermediate productivity is due to grazer control with selective feeding, which leads to the predator-mediated coexistence of prey. The negative slope at high productivity is due to seasonal blooms of opportunist species that occur before they are regulated by grazers. The negative side is only unveiled when the temporal scale of the observation captures the transient dynamics, which are especially relevant at highly seasonal latitudes. Thus selective predation explains the positive side while transient competitive exclusion explains the negative side of the unimodal PDR curve. The phytoplankton community composition of the positive and negative sides is mostly dominated by slow-growing nutrient specialists and fast-growing nutrient opportunist species, respectively. PMID:24980772
Vallina, S M; Follows, M J; Dutkiewicz, S; Montoya, J M; Cermeno, P; Loreau, M
Nannopus palustris Brady, 1880 is a free-living widely distributed harpacticoid copepod, which has been formerly assumed to be a single, cosmopolitan but highly variable species. We compared several geographically distant N. palustris populations in terms of their morphology and genetics. Populations from the White Sea (WS), the North Sea (NS), the Black Sea (BS) and two sympatric morphs from South Carolina, USA (SC notched and SC straight morphs), were considered. The NS, BS and to a lesser extent SC notched specimens were morphologically similar and partly coincided to the 'canonical' description of the species. By contrast, WS population showed remarkable anatomical and morphometric peculiarities that correspond to some earlier descriptions. Genetic analyses of mitochondrial (cytochrome b) and nuclear (28S rDNA) genes demonstrated the significant distinctness among WS, both SC and (NS+BS) populations, the latter two being genetically indistinguishable. Concordance between mitochondrial and nuclear gene trees and morphological data supports that N. palustris is in fact composed of several pseudo-sibling species, which are genetically and morphologically divergent. Neither correlation between genetic divergence and geographical distance nor significant intrapopulation diversity was found for these species. Taxonomic status, distribution and phylogenetic relationships of the species within the Nannopus genus need to be reconsidered. A further subdivision of species complexes might have important implications for the analysis of biodiversity of benthic copepods and consequently for the interpretation of their (species-specific) ecological function. PMID:22989315
Garlitska, Lesya; Neretina, Tatyana; Schepetov, Dimitry; Mugue, Nikolai; De Troch, Marleen; Baguley, Jeffrey G; Azovsky, Andrey
We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean Rj genotypes (non-Rj, Rj2Rj3, and Rj4). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA Bradyrhizobium strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were Bradyrhizobium japonicum Bj123, in the northern United States, and Bradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to B. elkanii than for the cluster belonging to B. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.
Shiro, Sokichi; Matsuura, Syota; Saiki, Rina; Sigua, Gilbert C.; Yamamoto, Akihiro; Umehara, Yosuke; Hayashi, Masaki
Plasmodium vivax merozoite surface protein-5 (PvMsp-5), a potential vaccine candidate, is encoded by a two-exon single copy gene. We have conducted a comprehensive analysis of PvMsp-5 by sequencing the entire gene of four parasite populations from northwestern Thailand (n = 73), southern Thailand (n = 53), Indonesia (n = 25) and Brazil (n = 24), and five isolates from other endemic areas. Results reveal that exon I exhibits a significantly higher level of nucleotide diversity at both synonymous and nonsynonymous sites than exon II (p < 0.01). Neutrality tests based on both intraspecific and interspecific nucleotide polymorphism have detected a signature of positive selection in exon I of all populations while substitutions in exon II mainly followed neutral expectation except that three residues in exon II of northwestern Thailand population appear to be positively selected using the Bayes Empirical Bayes method. Short imperfect repeats were identified in exon I at an equivalent region to its orthologue in P. knowlesi, supporting their close genetic relatedness. Significant levels of population subdivision were detected among most populations including those between northwestern and southern Thailand (p < 10?5), implying absent or minimal gene flow between these populations. Importantly, evidences for intragenic recombination in PvMsp-5 were found in most populations except that from southern Thailand in which haplotype diversity and nucleotide diversity were exceptionally low. Results from Fu and Li’s D*, F* and D and F tests suggested that PvMsp-5 of most P. vivax populations have been maintained by balancing selection whereas southern Thailand population could have gone through recent bottleneck events. These findings are concordant with a substantial reduction in number of P. vivax cases in southern Thailand during the past decade, followed by a very recent population expansion. Therefore, spatio-temporal monitoring of parasite population genetics provides important implications for disease control.
Putaporntip, Chaturong; Udomsangpetch, Rachanee; Pattanawong, Urassaya; Cui, Liwang; Jongwutiwes, Somchai
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
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
Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal.
Bojesen, Anders Miki; Torpdahl, Mia; Christensen, Henrik; Olsen, John Elmerdahl; Bisgaard, Magne
Amplified fragment length polymorphisms (AFLPs) were used to characterize the genotypic diversity of a total of 114 Gallibacterium anatis isolates originating from a reference collection representing 15 biovars from four countries and isolates obtained from tracheal and cloacal swab samples of chickens from an organic, egg-producing flock and a layer parent flock. A subset of strains was also characterized by pulsed-field gel electrophoresis and biotyping. The organic flock isolates were characterized by more than 94% genetic similarity, indicating that only a single clone was apparent in the flock. The layer parent flock isolates were grouped into two subclusters, each with similarity above 90%. One subcluster contained only tracheal isolates, while the other primarily included cloacal isolates. In conclusion, we show that AFLP analysis enables fingerprinting of G. anatis, which seems to have a clonal population structure within natural populations. There was further evidence of clonal lineages, which may have adapted to different sites within the same animal. PMID:12791918
Bojesen, Anders Miki; Torpdahl, Mia; Christensen, Henrik; Olsen, John Elmerdahl; Bisgaard, Magne
Genetic relationships among 79 strains of Escherichia coli, isolated mostly from diseased chickens, were estimated on the basis of allelic variation at 15 enzyme-encoding loci, determined by multilocus enzyme electrophoresis. All 15 loci were polymorphic, with an average of 4.1 allelic states per locus. Comparisons of the observed combinations of alleles among strains revealed 37 distinct multilocus genotypes that were used to define naturally occurring cell lineages or clones. Two-thirds of the isolates were classified into 10 clones, including a single multilocus genotype that accounted for about a third of all isolates. For isolates of these clones, there was a high concordance (76%) between identity in multilocus genotype, O:K:H serotype, and pattern of resistance to five antibiotics. Cluster analysis disclosed two major complexes of closely related clones, in which more than 50% of the isolates were associated with localized infections (airsacculitis and pericarditis). Both complexes contained isolates with serotype O2:K1, indicating that this serotype can occur on diverse chromosomal backgrounds. The results suggest that colibacillosis within avian populations is caused by a relatively limited number of pathogenic clones representing at least two distinct clone complexes.
Whittam, T S; Wilson, R A
Genetic diversity and genetic relationships among 42 Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, this P. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (IA) for the P. stutzeri strains analyzed was 1.10. The IA values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.
Rius, Nuria; Fuste, M. Carme; Guasp, Caterina; Lalucat, Jorge; Loren, Jose G.
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
Genetic diversity and relatedness between 2 geographically distant Holstein populations (in Luxembourg and Tunisia) were studied by pedigree analysis. These 2 populations have similar sizes and structures and are essentially importing populations. Edited pedigrees included 140,392 and 151,381 animals for Tunisia and Luxembourg, respectively. To partially account for pedigree completeness levels, a modified algorithm was used to compute inbreeding. The effective numbers of ancestors were derived from probabilities of gene origin for the 2 populations of cows born between 1990 and 2000. The 10 ancestors with the highest contributions to genetic diversity in the cow populations accounted for more than 32% of the genes. Eight of these 10 ancestors were the same in both populations. The rates of inbreeding were different in the 2 populations but were generally comparable to those found in the literature for the Holstein breed. Average inbreeding coefficients per year, estimated from the data, ranged from 0.91 and 0.50 in 1990 to 3.10 and 2.12 in 2000 for the Tunisian and Luxembourg populations, respectively. Genetic links have also strengthened with time. Average additive relationships between the 2 populations were as high as 2.2% in 2000. Results suggest that it would be possible to investigate genotype by environment interactions for milk traits using the Tunisian and Luxembourg dairy populations. PMID:17582137
Hammami, H; Croquet, C; Stoll, J; Rekik, B; Gengler, N
Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984–1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.
Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin
The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats. PMID:22537413
Yamada, Shuntaro; Ohkubo, Satoshi; Miyashita, Hideaki; Setoguchi, Hiroaki
This review covers the structures and genetics of the 46 O antigens of Salmonella, a major pathogen of humans and domestic animals. The variation in structures underpins the serological specificity of the 46 recognized serogroups. The O antigen is important for the full function and virulence of many bacteria, and the considerable diversity of O antigens can confer selective advantage. Salmonella O antigens can be divided into two major groups: those which have N-acetylglucosamine (GlcNAc) or N-acetylgalactosamine (GalNAc) and those which have galactose (Gal) as the first sugar in the O unit. In recent years, we have determined 21 chemical structures and sequenced 28 gene clusters for GlcNAc-/GalNAc-initiated O antigens, thus completing the structure and DNA sequence data for the 46 Salmonella O antigens. The structures and gene clusters of the GlcNAc-/GalNAc-initiated O antigens were found to be highly diverse, and 24 of them were found to be identical or closely related to Escherichia coli O antigens. Sequence comparisons indicate that all or most of the shared gene clusters were probably present in the common ancestor, although alternative explanations are also possible. In contrast, the better-known eight Gal-initiated O antigens are closely related both in structures and gene cluster sequences. PMID:23848592
Liu, Bin; Knirel, Yuriy A; Feng, Lu; Perepelov, Andrei V; Senchenkova, Sof'ya N; Reeves, Peter R; Wang, Lei
A set of 300 Dutch Cryptococcus neoformans isolates, obtained from 237 patients during 1977 to 2007, was investigated by determining the mating type, serotype, and AFLP and microsatellite genotype and susceptibility to seven antifungal compounds. Almost half of the studied cases were from HIV-infected patients, followed by a patient group of individuals with other underlying diseases and immunocompetent individuals. The majority of the isolates were mating type ? and serotype A, followed by ?D isolates and other minor categories. The most frequently observed genotype was AFLP1, distantly followed by AFLP2 and AFLP3. Microsatellite typing revealed a high genetic diversity among serotype A isolates but a lower diversity within the serotype D set of isolates. One patient was infected by multiple AFLP genotypes. Fluconazole and flucytosine had the highest geometric mean MICs of 2.9 and 3.5 ?g/ml, respectively, while amphotericin B (0.24 ?g/ml), itraconazole (0.08 ?g/ml), voriconazole (0.07 ?g/ml), posaconazole (0.06 ?g/ml), and isavuconazole (0.03 ?g/ml) had much lower geometric mean MICs. One isolate had a high flucytosine MIC (>64 ?g/ml), while decreased susceptibility (?16 ?g/ml) for flucytosine and fluconazole was found in 9 and 10 C. neoformans isolates, respectively. PMID:22442325
Hagen, Ferry; Illnait-Zaragozí, María-Teresa; Meis, Jacques F; Chew, William H M; Curfs-Breuker, Ilse; Mouton, Johan W; Hoepelman, Andy I M; Spanjaard, Lodewijk; Verweij, Paul E; Kampinga, Greetje A; Kuijper, Ed J; Boekhout, Teun; Klaassen, Corné H W
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
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
Microsatellite diversity was analyzed in four Proto-Australoid tribes, including Indo-European (Marathi)-speaking Katkari, Pawara, Mahadeo-Koli, and Dravidian (Gondi)-speaking groups of Maharashtra, west-central India, to understand their genetic structure and to identify the congruence between language and gene pool. Allele frequency data at 15 short tandem repeat (STR) loci in studied tribes was compared with data of 22 Indo-European- and Dravidian-speaking caste and tribal populations using heterozygosity, allele size variance, analysis of molecular variance (AMOVA), G(ST) estimate, PC plot, and Mantel correlation test. Our results demonstrate that "Gondi" tribes comprising the Madia-Gond, a hunter-gatherer population, and the agriculturist Dheria-Gond harbor lower diversity than "Marathi" tribal groups, which are culturally and genetically distinct. Katkari, a hunter-gatherer tribe, showed greater diversity and the presence of a large number of unique alleles, genetically distinct from all others except the Pawara, supporting their old cultural links. The agriculturist Pawara tribe represents a splinter subgroup of the Bhil tribe and has experienced gene flow. The Mahadeo-Koli, an agriculturally oriented tribe, displayed significant heterozygote deficiency, attributable to the practice of high endogamy. The Proto-Australoid tribal populations were genetically differentiated from castes of similar morphology, suggesting different evolutionary mechanisms operating upon the populations. The populations showed genetic and linguistic similarity, barring a few groups with varied migratory histories. The microsatellite variation clearly demonstrates the interplay of sociocultural factors including linguistic, geographical contiguity, and microevolutionary processes in shaping the genetic diversity of populations in contemporary India. This study supports the ethno-historical relationships of Indian populations. PMID:16323197
Gaikwad, Sonali; Vasulu, T S; Kashyap, V K
Leishmania infantum (syn. Leishmania chagasi) is the etiological agent of visceral leishmaniasis (VL) in Brazil. The epidemiology of VL is poorly understood. Therefore, a more detailed molecular characterization at an intraspecific level is certainly needed. Herein, three independent molecular methods, multilocus microsatellite typing (MLMT), random amplification of polymorphic DNA (RAPD) and simple sequence repeats-polymerase chain reaction (SSR-PCR), were used to evaluate the genetic diversity of 53 L. infantum isolates from five different endemic areas in Brazil. Population structures were inferred by distance-based and Bayesian-based approaches. Eighteen very similar genotypes were detected by MLMT, most of them differed in only one locus and no correlation was found between MLMT profiles, geographical origin or the estimated population structure. However, complex profiles composed of 182 bands obtained by both RAPD and SSR-PCR assays gave different results. Unweighted pair group method with arithmetic mean trees built from these data revealed a high degree of homogeneity within isolates of L. infantum. Interestingly, despite this genetic homogeneity, most of the isolates clustered according to their geographical origin. PMID:22310534
Segatto, Marcela; Ribeiro, Lucas Secchim; Costa, Dorcas Lamounier; Costa, Carlos Henrique Nery; Oliveira, Márcia Rosa de; Carvalho, Sílvio Fernando Guimarães; Macedo, Andréa Mara; Valadares, Helder Magno Silva; Dietze, Reynaldo; Brito, Cristiana Ferreira Alves de; Lemos, Elenice Moreira
Sea otters (Enhydra lutris) have been reported to become infected with Toxoplasma gondii and at times succumb to clinical disease. Here, we determined genotypes of 39 T. gondii isolates from 37 sea otters in two geographically distant locations (25 from California and 12 from Washington). Six genotypes were identified using 10 PCR-RFLP genetic markers including SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico, and by DNA sequencing of loci SAG1 and GRA6 in 13 isolates. Of these 39 isolates, 13 (33%) were clonal Type II which can be further divided into two groups at the locus Apico. Two of the 39 isolates had Type II alleles at all loci except a Type I allele at locus L358. One isolate had Type II alleles at all loci except the Type I alleles at loci L358 and Apico. One isolate had Type III alleles at all loci except Type II alleles at SAG2 and Apico. Two sea otter isolates had a mixed infection. Twenty-one (54%) isolates had an unique allele at SAG1 locus. Further genotyping or DNA sequence analysis for 18 of these 21 isolates at loci SAG1 and GRA6 revealed that there were two different genotypes, including the previously identified Type X (four isolates) and a new genotype named Type A (14 isolates). The results from this study suggest that the sea otter isolates are genetically diverse.
Sundar, N.; Cole, R. A.; Thomas, N. J.; Majumdar, D.; Dubey, J. P.; Su, C.
It has been argued that insect diversity in the Cape is disproportionately low, considering the unusually high plant diversity in this region. Recent studies have shown that this is not the case, but the precise mechanisms linking plant diversity and insect diversity in the Cape are still poorly understood. Here we use a dated genus-level phylogenetic tree of the Cape
?erban Proche?; Félix Forest; Ruan Veldtman; Steven L. Chown; Richard M. Cowling; Steven D. Johnson; David M. Richardson; Vincent Savolainen
African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics. PMID:24244771
Duffy, Craig W; MacLean, Lorna; Sweeney, Lindsay; Cooper, Anneli; Turner, C Michael R; Tait, Andy; Sternberg, Jeremy; Morrison, Liam J; MacLeod, Annette
Wild Dipsacus chinensis plants in China have become endangered owing to over-harvesting and habitat fragmentation. We examined the genetic diversity and genetic structure of 90 individuals from three populations using inter-simple sequence repeat markers and found that 106 of 173 bands amplified by 22 informative and reliable primers were polymorphic. These findings correspond to a medium level of genetic diversity. At the species level, the estimates of parameters of genetic diversity were as follows: polymorphic loci (61.27%); effective number of alleles (1.3873); Nei's genetic diversity (0.2202); Shannon's information index (0.3235). At the population level, the estimates were polymorphic loci (9.53%); effective number of alleles (1.0419); Nei's genetic diversity (0.0258); Shannon's information index (0.0402). Nei's coefficient of genetic differentiation was 0.8829, which is consistent with Shannon's coefficient of genetic differentiation (0.8757). Most of the genetic variation existed among populations, and some differentiation may have resulted from habitat fragmentation and barriers to gene flow (gene flow = 0.0663). Combining our results with those of on-site field investigation, we conclude that the present genetic diversity and genetic structure of natural populations of D. chinensis have been strongly affected by harvesting and habitat fragmentation. We also propose strategies for the conservation of this plant. PMID:23661445
Chen, D-X; Li, L-Y; Zhang, X; Wang, Y; Zhang, Z
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
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
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
BACKGROUND: Despite the two-fold cost of sex, most of the higher animals reproduce sexually. The advantage of sex has been suggested to be its ability, through recombination, to generate greater genetic diversity than asexuality, thus enhancing adaptation in a changing environment. We studied the genetic diversity and the population structure of three closely related species of bag worm moths: two
Alessandro Grapputo; Tomi Kumpulainen; Johanna Mappes; Silja Parri
Faba bean (Vicia faba L.), one of the most important legumes in the world, evolved different types of cultivars due to its partial cross-pollination. The development of simple sequence repeat (SSR) markers from expressed sequence tags (EST) provided a useful tool for investigation of its genetic diversity. The purpose of the present study was to investigate the genetic diversity of
Ya-ming GONG; Sheng-chun XU; Wei-hua MAO; Ze-yun LI; Qi-zan HU; Gu-wen ZHANG; Ju DING
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
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
Background and Aims Micronutrient malnutrition, particularly zinc and iron deficiency, afflicts over three billion people worldwide due to low dietary intake. In the current study, wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of domesticated wheat, was tested for (1) genetic diversity in grain nutrient concentrations, (2) associations among grain nutrients and their relationships with plant productivity, and (3) the association of grain nutrients with the eco-geographical origin of wild emmer accessions. Methods A total of 154 genotypes, including wild emmer accessions from across the Near Eastern Fertile Crescent and diverse wheat cultivars, were characterized in this 2-year field study for grain protein, micronutrient (zinc, iron, copper and manganese) and macronutrient (calcium, magnesium, potassium, phosphorus and sulphur) concentrations. Key Results Wide genetic diversity was found among the wild emmer accessions for all grain nutrients. The concentrations of grain zinc, iron and protein in wild accessions were about two-fold greater than in the domesticated genotypes. Concentrations of these compounds were positively correlated with one another, with no clear association with plant productivity, suggesting that all three nutrients can be improved concurrently with no yield penalty. A subset of 12 populations revealed significant genetic variation between and within populations for all minerals. Association between soil characteristics at the site of collection and grain nutrient concentrations showed negative associations between soil clay content and grain protein and between soil-extractable zinc and grain zinc, the latter suggesting that the greatest potential for grain nutrient minerals lies in populations from micronutrient-deficient soils. Conclusions Wild emmer wheat germplasm offers unique opportunities to exploit favourable alleles for grain nutrient properties that were excluded from the domesticated wheat gene pool.
Chatzav, Merav; Peleg, Zvi; Ozturk, Levent; Yazici, Atilla; Fahima, Tzion; Cakmak, Ismail; Saranga, Yehoshua
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
The prevalence of the newly discovered pneumococcal serotype 6C has increased in some countries since the introduction of seven-valent conjugate pneumococcal vaccine (PCV7). The distribution of invasive serogroup 6 serotypes, in Australia, including 6C and 6D, has not been reported previously. During the period 1999 to 2008, 6097 isolates were referred to the New South Wales Pneumococcal Reference Laboratory for serotyping. Of these, 847 were identified by Quellung reaction as belonging to serogroup 6 and 702 were available for further study. Serotypes were determined by serotype-specific PCR as follows: 6A, 197 (28.1%); 6B, 452 (64.4%); 6C, 52 (7.4%) and one 6D. The average numbers of invasive serogroup 6 isolates, per annum, fell from 62.2 before (2000-2005) to 49.7 after (2006-2008) the introduction of PCV7. The proportions of invasive 6B fell (from 72.4% to 47.3%, p 0.03), those of 6C rose (from 3.3% to 17%, p 0.02) significantly and those of 6A remained fairly constant (24.3% vs 27%, p 0.69) between the two periods. All 6C and 6D and selected 6A and 6B isolates were further characterized by multilocus sequence typing and sequence analysis of cps genes cpsA-cpsB (wzg-wzh) and wchA-wciN(beta) -wciO, wciP. Results showed considerable diversity within serotype 6C, apparently as a result of both mutation and recombination. Sequence typing indicates that, in Australia, 6C has been largely derived from 6A. The genetic diversity and rapid increase in incidence of serotype 6C causing invasive pneumococcal disease has potential implications for vaccine efficacy. PMID:20950338
Zhuo, F; Xiao, M; Kong, F; Oftadeh, S; Zhou, F; Zhang, J; Gilbert, G L
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
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.
Delay discounting is steeper for individuals who drink heavily or are alcohol dependent, but the reasons for this are unclear. Given the substantial genetic component for alcohol dependence it is not unreasonable to ask whether discounting and alcohol dependence have a genetic relationship. For there to be a genetic relationship, delay discounting must have a genetic component (heritability). A review of the human and animal literature suggests that this is the case. Other literature examining whether discounting is a correlated phenotype in individuals who are genetically predisposed to drink (family history positive individuals and selected lines of rats and mice) is mixed, suggesting that networks of genes are critical for the relationship to be seen. The identities of the genes in this network are not yet known, but research examining polymorphisms associated with differences in discounting is beginning to address this issue.
Mitchell, Suzanne H.
By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire. PMID:18000891
Ibarra-Rivera, Lisa; Mirabal, Sheyla; Regueiro, Manuela M; Herrera, Rene J
Population structure and genetic diversity in the Portuguese native breeds of pigs Alentejano (AL), Bísaro (BI), and Malhado de Alcobaça (MA) and the exotic breeds Duroc (DU), Landrace (LR), Large White (LW), and Pietrain were analyzed by typing 22 microsatellite markers in 249 individuals. In general, the markers used were greatly polymorphic, with mean total and effective number of alleles per locus of 10.68 and 4.33, respectively, and an expected heterozygosity of 0.667 across loci. The effective number of alleles per locus and expected heterozygosity were greatest in BI, LR, and AL, and least in DU. Private alleles were found in 9 of the 22 markers analyzed, mostly in AL, but also in the other breeds, with the exception of LW. The proportion of loci not in Hardy-Weinberg equilibrium in each breed analyzed ranged between 0.23 (AL) and 0.41 (BI, LW, and Pietrain), mostly because of a less than expected number of heterozygotes in those loci. With the exception of MA, all breeds showed a significant deficit in heterozygosity (F(IS); P < 0.05), which was more pronounced in BI (F(IS) = 0.175) and AL (F(IS) = 0.139), suggesting that inbreeding is a major concern, especially in these breeds that have gone through a genetic bottleneck in the recent past. The analysis of relationships among breeds, assessed by different methods, indicates that DU and AL are the more distanced breeds relative to the others, with the closest relationship being observed between LR and MA. The degree of differentiation between subpopulations (F(ST)) indicates that 0.184 of the total genetic variability can be attributed to differences among breeds. The analysis of individual distances based on allele sharing indicates that animals of the same breed generally cluster together, but subdivision is observed in the BI and LR breeds. Furthermore, the analysis of population structure indicates there is very little admixture among breeds, with each one being identified with a single ancestral population. The results of this study confirm that native breeds of pigs represent a very interesting reservoir of allelic diversity, even though the current levels of inbreeding raise concerns. Therefore, appropriate conservation efforts should be undertaken, such as adopting strategies aimed at minimizing inbreeding, to avoid further losses of genetic diversity. PMID:18567729
Vicente, A A; Carolino, M I; Sousa, M C O; Ginja, C; Silva, F S; Martinez, A M; Vega-Pla, J L; Carolino, N; Gama, L T
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup.
Akouamba, Bertine S.; Viel, Janique; Charest, Hugues; Merindol, Natacha; Samson, Johanne; Lapointe, Normand; Brenner, Bluma G.; Lalonde, Richard; Harrigan, P. Richard; Boucher, Marc
Feline morbillivirus (FmoPV) is an emerging virus in domestic cats and considered to be associated with tubulointerstitial nephritis. Although FmoPV was first described in China in 2012, there has been no report of the isolation of this virus in other countries. In this report, we describe the isolation and characterization of FmoPV from domestic cats in Japan. By using reverse transcription (RT)-PCR, we found that three of 13 urine samples from cats brought to veterinary hospitals were positive for FmoPV. FmoPV strains SS1 to SS3 were isolated from the RT-PCR-positive urine samples. Crandell-Rees feline kidney (CRFK) cells exposed to FmoPV showed cytopathic effects with syncytia formation, and FmoPV N protein was detected by indirect immunofluorescence assays. In addition, pleomorphic virus particles with apparent glycoprotein envelope spikes were observed by electron microscopy. By sequence analysis of FmoPV H and L genes, we found that FmoPVs showed genetic diversity; however, signatures of positive selection were not identified. PMID:24728711
Sakaguchi, Shoichi; Nakagawa, So; Yoshikawa, Rokusuke; Kuwahara, Chieko; Hagiwara, Hiroko; Asai, Ken-Ichi; Kawakami, Kazuo; Yamamoto, Yu; Ogawa, Makoto; Miyazawa, Takayuki
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.
More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852?bp of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals was 34.0%. The probability of Bartonella infection varied significantly with species, sex, sexual condition, and some locality, but not with season, elevation, habitat type, animal weight, and ectoparasite infestation. In total, we found 18 unique Bartonella genotypes clustered into 5 clades, 1 clade exclusively Ethiopian, 2 clades clustered with genotypes from central and eastern Africa, and the remaining 2 clades clustered with genotypes and species from Africa and Asia. The close relatedness of several of our Bartonella genotypes obtained from the 3 dominant rodent species in Tigray with the pathogenic Bartonella elizabethae from Rattus spp. in Asia indicates a potential public health threat. PMID:23421888
Meheretu, Yonas; Leirs, Herwig; Welegerima, Kiros; Breno, Matteo; Tomas, Zewdneh; Kidane, Dawit; Girmay, Kokob; de Bellocq, Joëlle Goüy
Blastocystis is a common unicellular anaerobic eukaryote that inhabits the large intestine of many animals worldwide, including humans. The finding of Blastocystis in faeces in mammals and birds has led to proposals of zoonotic potential and that these hosts may be the source of many human infections. Blastocystis is, however, a genetically diverse complex of many distinct organisms (termed subtypes; STs), and sampling to date has been limited, both geographically and in the range of hosts studied. In order to expand our understanding of host specificity of Blastocystis STs, 557 samples were examined from various non-primate animal hosts and from a variety of different countries in Africa, Asia and Europe. STs were identified using 'barcoding' of the small subunit rRNA gene using DNA extracted either from culture or directly from faeces. The host and geographic range of several STs has thereby been greatly expanded and the evidence suggests that livestock is not a major contributor to human infection. Two new STs were detected among the barcode sequences obtained; for these, and for three others where the data were incomplete, the corresponding genes were fully sequenced and phylogenetic analysis was undertaken. PMID:23770574
Alfellani, Mohammed A; Taner-Mulla, Derya; Jacob, Alison S; Imeede, Christine Atim; Yoshikawa, Hisao; Stensvold, C Rune; Clark, C Graham
A total of 166 faecal specimens from diarrheic cattle were collected in China for detection of bovine kobuvirus (BKV) by reverse transcription PCR (RT-PCR) targeting the region a portion of the 3D nonstructural protein, with an amplicon size of 631 bp. The RNA corresponding to the BKV 3D region was detected in 34.9 % of faecal samples (58/166) in four major dairy-cattle-production areas in China, and sequence analysis based on the partial 3D sequences (35/58) indicated that the Chinese BKVs shared 88.9-96.2 % nucleotide sequence identity to BKV reference strains. Further phylogenetic analysis based on the complete VP1-encoding sequences (17/35) revealed that the Chinese BKVs shared 81-83.4 % nucleotide sequence identity to the U-1 strain, and these Chinese BKV strains, together with the U-1 strain, are apparently divided into four lineages, representing four genotypes of BKV, designated as A, B, C and D. Our results show that BKV infection is widely distributed, with high genetic diversity in China. PMID:24366549
Chang, Jitao; Wang, Qian; Wang, Fang; Jiang, Zhigang; Liu, Yue; Yu, Li
The evolutionary history of the Mycobacterium tuberculosis complex (MTBC) has previously been studied by analysis of sequence diversity in extant strains, but not addressed by direct examination of strain genotypes in archaeological remains. Here, we use ancient DNA sequencing to type 11 single nucleotide polymorphisms and two large sequence polymorphisms in the MTBC strains present in 10 archaeological samples from skeletons from Britain and Europe dating to the second-nineteenth centuries AD. The results enable us to assign the strains to groupings and lineages recognized in the extant MTBC. We show that at least during the eighteenth-nineteenth centuries AD, strains of M. tuberculosis belonging to different genetic groups were present in Britain at the same time, possibly even at a single location, and we present evidence for a mixed infection in at least one individual. Our study shows that ancient DNA typing applied to multiple samples can provide sufficiently detailed information to contribute to both archaeological and evolutionary knowledge of the history of tuberculosis. PMID:24573854
Müller, Romy; Roberts, Charlotte A; Brown, Terence A
Pigeon circovirus (PiCV) is an immunosuppressive agent widespread throughout the world, which causes a disease in pigeons called Young Pigeon Disease Syndrome. The aim of the study was to evaluate the prevalence of PiCV in Poland and investigate the genetic diversity relative to other known PiCV isolates. Samples from 152 pigeon flocks (88 flocks of racing pigeons and 64 flocks of fancy pigeons) from various regions of Poland were tested by polymerase chain reaction and an approximately 326-base fragment of the capsid protein gene (Cap gene) of the virus was amplified. The average viral prevalence was found to be 70.3% (76.13% in racing pigeons and 62.5% in fancy pigeons). Among the obtained positive samples, 21 were selected for sequencing and a phylogenetic analysis was performed. It was found that the majority of Polish PiCV isolates, to varying degrees, are related to isolates occurring in Europe. It was also observed that the Cap gene is variable and mutations often occur in it, which impacts the amino acid sequences in the capsid protein (nucleotide similarity averaged 86.57%, amino acid similarity averaged 89.02%). PMID:24659711
Stenzel, Tomasz; Pestka, Daria
A rice mini-core collection consisting of 217 accessions has been developed to represent the USDA core and whole collections that include 1,794 and 18,709 accessions, respectively. To improve the efficiency of mining valuable genes and broadening the genetic diversity in breeding, genetic structure and diversity were analyzed using both genotypic (128 molecular markers) and phenotypic (14 numerical traits) data. This mini-core had 13.5 alleles per locus, which is the most among the reported germplasm collections of rice. Similarly, polymorphic information content (PIC) value was 0.71 in the mini-core which is the highest with one exception. The high genetic diversity in the mini-core suggests there is a good possibility of mining genes of interest and selecting parents which will improve food production and quality. A model-based clustering analysis resulted in lowland rice including three groups, aus (39 accessions), indica (71) and their admixtures (5), upland rice including temperate japonica (32), tropical japonica (40), aromatic (6) and their admixtures (12) and wild rice (12) including glaberrima and four other species of Oryza. Group differentiation was analyzed using both genotypic distance Fst from 128 molecular markers and phenotypic (Mahalanobis) distance D(2) from 14 traits. Both dendrograms built by Fst and D(2) reached similar-differentiative relationship among these genetic groups, and the correlation coefficient showed high value 0.85 between Fst matrix and D(2) matrix. The information of genetic and phenotypic differentiation could be helpful for the association mapping of genes of interest. Analysis of genotypic and phenotypic diversity based on genetic structure would facilitate parent selection for broadening genetic base of modern rice cultivars via breeding effort. PMID:21080033
Li, Xiaobai; Yan, Wengui; Agrama, Hesham; Hu, Biaolin; Jia, Limeng; Jia, Melissa; Jackson, Aaron; Moldenhauer, Karen; McClung, Anna; Wu, Dianxing
Background Implementation of molecular breeding in rye (Secale cereale L.) improvement programs depends on the availability of high-density molecular linkage maps. However, the number of sequence-specific PCR-based markers available for the species is limited. Diversity Arrays Technology (DArT) is a microarray-based method allowing for detection of DNA polymorphism at several thousand loci in a single assay without relying on DNA sequence information. The objective of this study was the development and application of Diversity Arrays technology for rye. Results Using the PstI/TaqI method of complexity reduction we created a rye diversity panel from DNA of 16 rye varieties and 15 rye inbred lines, including parents of a mapping population consisting of 82 recombinant inbred lines. The usefulness of a wheat diversity panel for identification of DArT markers for rye was also demonstrated. We identified 1022 clones that were polymorphic in the genotyped ILs and varieties and 1965 clones that differentiated the parental lines L318 and L9 and segregated in the mapping population. Hierarchical clustering and ordination analysis were performed based on the 1022 DArT markers to reveal genetic relationships between the rye varieties and inbred lines included in the study. Chromosomal location of 1872 DArT markers was determined using wheat-rye addition lines and 1818 DArT markers (among them 1181 unique, non-cosegregating) were placed on a genetic linkage map of the cross L318 × L9, providing an average density of one unique marker every 2.68 cM. This is the most saturated rye linkage map based solely on transferable markers available at the moment, providing rye breeders and researches with a better choice of markers and a higher probability of finding polymorphic markers in the region of interest. Conclusion The Diversity Arrays Technology can be efficiently and effectively used for rye genome analyses - assessment of genetic similarity and linkage mapping. The 11520-clone rye genotyping panel with several thousand markers with determined chromosomal location and accessible through an inexpensive genotyping service is a valuable resource for studies on rye genome organization and in molecular breeding of the species.
Diversity analyses in alfalfa have mainly evaluated genetic relationships of cultivated germplasm, with little known about variation in diploid germplasm in the M. sativa-falcata complex. A collection of 374 individual genotypes derived from 120 unimproved diploid accessions from the National Plant Germplasm System, including M. sativa subsp. caerulea, falcata, and hemicycla, were evaluated with 89 polymorphic SSR loci in order to estimate genetic diversity, infer the genetic bases of current morphology-based taxonomy, and determine population structure. Diploid alfalfa is highly variable. A model-based clustering analysis of the genomic data identified two clearly discrete subpopulations, corresponding to the morphologically defined subspecies falcata and caerulea, with evidence of the hybrid nature of the subspecies hemicycla based on genome composition. Two distinct subpopulations exist within each subsp. caerulea and subsp. falcata. The distinction of caerulea was based on geographical distribution. The two falcata groups were separated based on ecogeography. The results show that taxonomic relationships based on morphology are reflected in the genetic marker data with some exceptions, and that clear distinctions among subspecies are evident at the diploid level. This research provides a baseline from which to systematically evaluate variability in tetraploid alfalfa and serves as a starting point for exploring diploid alfalfa for genetic and breeding experiments. PMID:20352180
Sakiro?lu, Muhammet; Doyle, Jeffrey J; Charles Brummer, E
GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found. PMID:24795369
Gillis, Annika; Mahillon, Jacques
Dramatic changes in the North American landscape over the last 12?000 years have shaped the genomes of the small mammals, such as the white-footed mouse (Peromyscus leucopus), which currently inhabit the region. However, very recent interactions of populations with each other and the environment are expected to leave the most pronounced signature on rapidly evolving nuclear microsatellite loci. We analyzed landscape characteristics and microsatellite markers of P. leucopus populations along a transect from southern Ohio to northern Michigan, in order to evaluate hypotheses about the spatial distribution of genetic heterogeneity. Genetic diversity increased to the north and was best approximated by a single-variable model based on habitat availability within a 0.5-km radius of trapping sites. Interpopulation differentiation measured by clustering analysis was highly variable and not significantly related to latitude or habitat availability. Interpopulation differentiation measured as FST values and chord distance was correlated with the proportion of habitat intervening, but was best explained by agricultural distance and by latitude. The observed gradients in diversity and interpopulation differentiation were consistent with recent habitat availability being the major constraint on effective population size in this system, and contradicted the predictions of both the postglacial expansion and core-periphery hypotheses. PMID:24448564
Taylor, Z S; Hoffman, S M G
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
This study used morphological characterization and phylogenetic analysis of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA to investigate the phylogeny of Passiflora species. The samples were collected from various regions of East Malaysia, and discriminant function analysis based on linear combinations of morphological variables was used to classify the Passiflora species. The biplots generated five distinct groups discriminated by morphological variables. The group consisted of cultivars of P. edulis with high levels of genetic similarity; in contrast, P. foetida was highly divergent from other species in the morphological biplots. The final dataset of aligned sequences from nine studied Passiflora accessions and 30 other individuals obtained from GenBank database (NCBI) yielded one most parsimonious tree with two strongly supported clades. Maximum parsimony (MP) tree showed the phylogenetic relationships within this subgenus Passiflora support the classification at the series level. The constructed phylogenic tree also confirmed the divergence of P. foetida from all other species and the closeness of wild and cultivated species. The phylogenetic relationships were consistent with results of morphological assessments. The results of this study indicate that ITS region analysis represents a useful tool for evaluating genetic diversity in Passiflora at the species level.
Ramaiya, Shiamala Devi; Bujang, Japar Sidik; Zakaria, Muta Harah
Multilocus enzyme electrophoresis was used to examine genetic relationships among and between toxigenic and non-toxigenic isolates of Vibrio cholerae O1 obtained from patients and the environment in the US Gulf Coast and surrounding areas. A total of 23 toxigenic and 23 non-toxigenic strains were examined. All the toxigenic and 7 of the non-toxigenic strains had the same alleles at 16 enzyme loci, whereas the balance of the nontoxigenic strains had 9 distinct combinations of alleles. This study suggests that all of the toxigenic strains belong to a single clone, and that while some of the non-toxigenic isolates were related, most were of diverse origin. PMID:1879486
Chen, F; Evins, G M; Cook, W L; Almeida, R; Hargrett-Bean, N; Wachsmuth, K
The genus Labisia (Myrsinaceae) is a popular medicinal plant in Malaysia. We examined the genetic relationship among three varieties of L. pumila var. pumila, L. pumila var. alata, L. pumila var. lanceolata and Labisia paucifolia using an ISSR assay. Fifty-eight primers were tested, among which 18 gave reliable polymorphic banding patterns; these yielded 264 polymorphic markers. A similarity matrix was used to construct a dendrogram, and a principal component plot was developed to examine genetic relationships among varieties. Jaccard's similarity coefficient among species ranged from 0.09 to 0.14. At a similarity of 0.117%, species were divided into two main clusters. The mean value of the observed number of alleles, the effective number of alleles, mean Nei's gene diversity, and Shannon's information index were 1.98, 1.64, 0.38, and 0.57, respectively. PMID:24841662
Karimi, E; Jaafar, H Z E; Aziz, M A; Taheri, S; AzadiGonbad, R
Genetic relationships among 40 loquat (Eriobotrya japonica (Thunb) Lindl) accessions that originated from different countries and that are part of the germplasm collection of the Instituto Valenciano de Investigaciones Agrarias (IVIA) (Valencia, Spain) were evaluated using microsatellites. Thirty primer pairs flanking microsatellites previously identified in Malus x domestica (Borkh.) were assayed. Thirteen of them amplified polymorphic products and unambiguously distinguished 34 genotypes from the 40 accessions analyzed. Six accessions showing identical marker patterns were Spanish local varieties thought to have been derived from 'Algerie' by a mutational process very common in loquat species. A total of 39 alleles were detected in the population studied, with a mean value of 2.4 alleles per locus. The expected and observed heterozygosities were 0.46 and 51% on average, respectively, leading to a negative value of the Wright's fixation index (-0.20). The values of these parameters indicate a smaller degree of genetic diversity in the set of loquat accessions analyzed than in other members of the Rosaceae family. Unweighted pair-group method (UPGMA) cluster analysis, based on Nei's genetic distance, generally grouped genotypes according to their geographic origins and pedigrees. The high number of alleles and the high expected heterozygosity detected with SSR markers developed in Malus x domestica (Borkh.) make them a suitable tool for loquat cultivar identification, confirming microsatellite marker transportability among genera in the Rosaceae family. PMID:15729402
Soriano, José Miguel; Romero, Carlos; Vilanova, Santiago; Llácer, Gerardo; Badenes, María Luisa
Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships.
Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.
This study was conducted to establish genetic criteria for phenotypic characteristics of Hanwoo cattle based on allele frequencies and genetic variance analysis using microsatellite markers. Analysis of the genetic diversity among 399 Hanwoo cattle classified according to nose pigmentation and coat color was carried out using 22 microsatellite markers. The results revealed that the INRA035 locus was associated with the highest Fis (0.536). Given that the Fis value for the Hanwoo INRA035 population ranged from 0.533 (white) to 1.000 (white spotted), this finding was consistent with the loci being fixed in Hanwoo cattle. Expected heterozygosities of the Hanwoo groups classified by coat colors and degree of nose pigmentation ranged from 0.689±0.023 (Holstein) to 0.743±0.021 (nose pigmentation level of d). Normal Hanwoo and animals with a mixed white coat showed the closest relationship because the lowest DA value was observed between these groups. However, a pair-wise differentiation test of Fst showed no significant difference among the Hanwoo groups classified by coat color and degree of nose pigmentation (p<0.01). Moreover, results of the neighbor-joining tree based on a DA genetic distance matrix within 399 Hanwoo individuals and principal component analyses confirmed that different groups of cattle with mixed coat color and nose pigmentation formed other specific groups representing Hanwoo genetic and phenotypic characteristics. The results of this study support a relaxation of policies regulating bull selection or animal registration in an effort to minimize financial loss, and could provide basic information that can be used for establishing criteria to classify Hanwoo phenotypes.
Choi, T. J.; Lee, S. S.; Yoon, D. H.; Kang, H. S.; Kim, C. D.; Hwang, I. H.; Kim, C. Y.; Jin, X.; Yang, C. G.; Seo, K. S.
College diversity experiences have been praised not only for their role in promoting student growth but also for contributing to future engagement with diversity. However, the evidence supporting this latter claim is quite limited, often relying on cross-sectional analyses. This study examines whether and how students' first-year diversity…
Bowman, Nicholas A.
The DNA fingerprint and genetic relationship of 6 Indian goat breeds were studied by RAPD technique. Intra- and inter-breed divergence was estimated in terms of band sharing frequency (BSF) and mean average percentage difference (MAPD). The interbreed BSF was lower than intrabreed BSF due to more homogeneity within breed than between breeds. Inter reed BSF showed more similarity between Marwari
Anita Yadav; B R Yadav
Genetic and environmental factors underlying relationships between personality traits and disordered eating were examined in 256 female adolescent twin pairs (166 monozygotic, 90 dizygotic). Eating behaviors were assessed with the Total Score, Body Dissatisfaction, Weight Preoccupation, Binge Eating, and Compensatory Behavior subscales from the Minnesota Eating Disorders Inventory (M-EDI; K. L. Klump, M. McGue, & W. G. Iacono, 2000). Personality
Kelly L. Klump; Matt McGue; William G. Iacono
Background The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. Results The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. Conclusions The results reported improve our understanding of the combined effects of geography, ecology and human intervention on organization of the C. baccatum genepool. The results will facilitate utilization of C. baccatum for crop improvement and species conservation by providing a framework for efficient germplasm collection management and guidance for future plant acquisitions.
The issue of loss of animal genetic diversity, worldwide in general and in Canada in particular, has become noteworthy. The objective of this study was to analyze the trend in within-breed genetic diversity and identify the major causes of loss of genetic diversity in five Canadian dairy breeds. Pedigrees were analyzed using the software EVA (evolutionary algorithm) and CFC (contribution, inbreeding, coancestry), and a FORTRAN package for pedigree analysis suited for large populations (PEDIG). The average rate of inbreeding in the last generation analyzed (2003 to 2007) was 0.93, 1.07, 1.26, 1.09 and 0.80% for Ayrshire, Brown Swiss, Canadienne, Guernsey and Milking Shorthorn, respectively, and the corresponding estimated effective population sizes were 54, 47, 40, 46 and 66, respectively. Based on coancestry coefficients, the estimated effective population sizes in the last generation were 62, 76, 43, 61 and 76, respectively. The estimated percentage of genetic diversity lost within each breed over the last four decades was 6, 7, 11, 8 and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the five breeds ranged between 59.3% and 89.7%. The results indicate that each breed has lost genetic diversity over time and that the loss is gaining momentum due to increasing rates of inbreeding and reduced effective population sizes. Therefore, strategies to decrease rate of inbreeding and increase the effective population size are advised. PMID:24079800
Melka, M G; Stachowicz, K; Miglior, F; Schenkel, F S
'Fire mosaics' are often maintained in landscapes to promote successional diversity in vegetation with little understanding of how this will affect ecological processes in animal populations such as dispersal, social organization and re-establishment. To investigate these processes, we conducted a replicated, spatiotemporal landscape genetics study of two Australian woodland lizard species [Amphibolurus norrisi (Agamidae) and Ctenotus atlas (Scincidae)]. Agamids have a more complex social and territory structure than skinks, so fire might have a greater impact on their population structure and thus genetic diversity. Genetic diversity increased with time since fire in C. atlas and decreased with time since fire in A. norrisi. For C. atlas, this might reflect its increasing population size after fire, but we could not detect increased gene flow that would reduce the loss of genetic diversity through genetic drift. Using landscape resistance analyses, we found no evidence that postfire habitat succession or topography affected gene flow in either species and we were unable to distinguish between survival and immigration as modes of postfire re-establishment. In A. norrisi, we detected female-biased dispersal, likely reflecting its territorial social structure and polygynous mating system. The increased genetic diversity in A. norrisi in recently burnt habitat might reflect a temporary disruption of its territoriality and increased male dispersal, a hypothesis that was supported with a simulation experiment. Our results suggest that the effects of disturbance on genetic diversity will be stronger for species with territorial social organization. PMID:24750427
Smith, Annabel L; Bull, C Michael; Gardner, Michael G; Driscoll, Don A
Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA)-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups), six (containing 99% of all the sequences) belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus), and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally. PMID:23024768
Guo, Zhiling; Liu, Sheng; Hu, Simin; Li, Tao; Huang, Yousong; Liu, Guangxing; Zhang, Huan; Lin, Senjie
Toward understanding the genetic diversity and distribution of copepod-associated symbiotic ciliates and the evolutionary relationships with their hosts in the marine environment, we developed a small subunit ribosomal RNA gene (18S rDNA)-based molecular method and investigated the genetic diversity and genotype distribution of the symbiotic ciliates on copepods. Of the 10 copepod species representing six families collected from six locations of Pacific and Atlantic Oceans, 9 were found to harbor ciliate symbionts. Phylogenetic analysis of the 391 ciliate 18S rDNA sequences obtained revealed seven groups (ribogroups), six (containing 99% of all the sequences) belonging to subclass Apostomatida, the other clustered with peritrich ciliate Vorticella gracilis. Among the Apostomatida groups, Group III were essentially identical to Vampyrophrya pelagica, and the other five groups represented the undocumented ciliates that were close to Vampyrophrya/Gymnodinioides/Hyalophysa. Group VI ciliates were found in all copepod species but one (Calanus sinicus), and were most abundant among all ciliate sequences obtained, indicating that they are the dominant symbiotic ciliates universally associated with copepods. In contrast, some ciliate sequences were found only in some of the copepods examined, suggesting the host selectivity and geographic differentiation of ciliates, which requires further verification by more extensive sampling. Our results reveal the wide occurrence and high genetic diversity of symbiotic ciliates on marine copepods and highlight the need to systematically investigate the host- and geography-based genetic differentiation and ecological roles of these ciliates globally.
Guo, Zhiling; Liu, Sheng; Hu, Simin; Li, Tao; Huang, Yousong; Liu, Guangxing; Zhang, Huan; Lin, Senjie
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
Background Patterns of genetic diversity between and within natural plant populations and their driving forces are of great interest in evolutionary biology. However, few studies have been performed on the genetic structure and population divergence in wild emmer wheat using a large number of EST-related single nucleotide polymorphism (SNP) markers. Results In the present study, twenty-five natural wild emmer wheat populations representing a wide range of ecological conditions in Israel and Turkey were used. Genetic diversity and genetic structure were investigated using over 1,000 SNP markers. A moderate level of genetic diversity was detected due to the biallelic property of SNP markers. Clustering based on Bayesian model showed that grouping pattern is related to the geographical distribution of the wild emmer wheat. However, genetic differentiation between populations was not necessarily dependent on the geographical distances. A total of 33 outlier loci under positive selection were identified using a FST-outlier method. Significant correlations between loci and ecogeographical factors were observed. Conclusions Natural selection appears to play a major role in generating adaptive structures in wild emmer wheat. SNP markers are appropriate for detecting selectively-channeled adaptive genetic diversity in natural populations of wild emmer wheat. This adaptive genetic diversity is significantly associated with ecological factors.
The presence, genetic identity and diversity of algal endosymbionts ( Symbiodinium ) in 114 species from 69 genera (20 families) of octocorals from the Great Barrier Reef (GBR), the far eastern Pacific (EP) and the Caribbean was examined, and patterns of the octocoral-algal symbiosis were compared with patterns in the host phylogeny. Genetic analyses of the zooxanthellae were based on
M. J. H. V AN; J. C. M IEOG OPPEN; K. E. FABRICIUS
Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.
Lum, J K; Cann, R L; Martinson, J J; Jorde, L B
Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis. PMID:24814796
Crauwels, Sam; Zhu, Bo; Steensels, Jan; Busschaert, Pieter; De Samblanx, Gorik; Marchal, Kathleen; Willems, Kris A; Verstrepen, Kevin J; Lievens, Bart
The genus Echinacea is comprised of nine species, which are perennial herbs indigenous to North America and which have been traditionally used as medicinal plants for centuries. Three Echinacea species, E. angustifolia, E. purpurea, and E. pallida, are currently being traded internationally in the natural products market. Echinacea products constitute a significant portion of this growing, multi-billion dollar industry. The
J. Kapteyn; P. B. Goldsbrough; J. E. Simon
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.
The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism\\u000a was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent\\u000a natural populations, this intra-ecotypic diversity reflects natural genetic
P. Breyne; D. Rombaut; A. Van Gysel; M. Van Montagu; T. Gerats
Field experiments were conducted in 2005 in the Experimental Farm Station of the University of Agriculture. Makurdi, Nigeria to evaluate the performance and genetic diversity of some upland rice accessions. Preliminary results indicates highly significant (P<0.01) differences on all traits studied except for grain length, grain width, grain length\\/width ratio and 1000 grain weight, indicating genetic diversity among these accessions.
This study explored the relationship between riverine physical complexity, as determined from remotely sensed metrics, and anadromy and genetic diversity in steelhead or rainbow trout Oncorhynchus mykiss. The proportion of anadromy (estimated fraction of individuals within a drainage that are anadromous) was correlated with riverine complexity, but this correlation appeared to be driven largely by a confounding negative relationship between drainage area and the proportion of anadromy. Genetic diversity decreased with latitude, was lower in rivers with only non-anadromous individuals and also decreased with an increasing ratio of floodplain area to total drainage area. Anadromy may be less frequent in larger drainages due to the higher cost of migration associated with reaches farther from the ocean, and the negative relationship between genetic diversity and floodplain area may be due to lower effective population size resulting from greater population fluctuations associated with higher rates of habitat turnover. Ultimately, the relationships between riverine physical complexity and migratory life history or genetic diversity probably depend on the spatial scale of analysis. PMID:24766581
McPhee, M V; Whited, D C; Kuzishchin, K V; Stanford, J A
The relationship between biological network architectures and evolution is unclear. Within the phylum nematoda olfaction represents a critical survival tool. For nematodes, olfaction contributes to multiple processes including the finding of food, hosts, and reproductive partners, making developmental decisions, and evading predators. Here we examine a dynamic nematode odor genetic network to investigate how divergence, diversity, and contribution are shaped by network topology. Our findings describe connectivity frameworks and characteristics that correlate with molecular evolution and contribution across the olfactory network. Our data helps guide the development of a robust evolutionary description of the nematode odor network that may eventually aid in the prediction of interactive and functional qualities of novel nodes.
Fitzpatrick, David A.; O'Halloran, Damien M.
Recent losses of honey bee colonies have led to increased interest in the microbial communities that are associated with these important pollinators. A critical function that bacteria perform for their honey bee hosts, but one that is poorly understood, is the transformation of worker-collected pollen into bee bread, a nutritious food product that can be stored for long periods in colonies. We used 16S rRNA pyrosequencing to comprehensively characterize in genetically diverse and genetically uniform colonies the active bacterial communities that are found on honey bees, in their digestive tracts, and in bee bread. This method provided insights that have not been revealed by past studies into the content and benefits of honey bee-associated microbial communities. Colony microbiotas differed substantially between sampling environments and were dominated by several anaerobic bacterial genera never before associated with honey bees, but renowned for their use by humans to ferment food. Colonies with genetically diverse populations of workers, a result of the highly promiscuous mating behavior of queens, benefited from greater microbial diversity, reduced pathogen loads, and increased abundance of putatively helpful bacteria, particularly species from the potentially probiotic genus Bifidobacterium. Across all colonies, Bifidobacterium activity was negatively correlated with the activity of genera that include pathogenic microbes; this relationship suggests a possible target for understanding whether microbes provide protective benefits to honey bees. Within-colony diversity shapes microbiotas associated with honey bees in ways that may have important repercussions for colony function and health. Our findings illuminate the importance of honey bee-bacteria symbioses and examine their intersection with nutrition, pathogen load, and genetic diversity, factors that are considered key to understanding honey bee decline.
Mattila, Heather R.; Rios, Daniela; Walker-Sperling, Victoria E.; Roeselers, Guus; Newton, Irene L. G.
The fitness of species with little genetic diversity is expected to be affected by inbreeding and an inability to respond to environmental change. Conservation theory suggests that endangered species will generally demonstrate lower genetic diversity than taxa that are not threatened. This hypothesis has been challenged because the time frame of anthropogenic extinction may be too fast to expect genetic factors to significantly contribute. I conducted a meta-analysis to examine how genetic diversity in 894 tetrapods correlates with extinction threat level. Because species are not evolutionarily independent, I used a phylogenetic regression framework to address this issue. Mean genetic diversity of tetrapods, as assessed by protein heterozygosity, was 29.7–31.5% lower on average in threatened species than in their nonthreatened relatives, a highly significant reduction. Within amphibians as diversity decreased extinction risk increased in phylogenetic models, but not in nonphylogenetic regressions. The effects of threatened status on diversity also remained significant after accounting for body size in mammals. These results support the hypothesis that genetic effects on population fitness are important in the extinction process.
FLIGHT, PATRICK A.
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
We examined sequence variation in the control region of the mitochondrial genome from 778 seals sampled at 161 locations from northern Japan to southeastern Alaska to learn more about the evolutionary history and population structure of, and effects of recent declines on genetic diversity in, harbor seals ( Phoca vitulina) in the northern Pacific Ocean. High haplotypic diversity (H 5
Robin L. Westlake; Gregory M. O'Corry-Crowe
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
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
Ballota undulata, Ballota kaiseri, and Ballota saxatilis are very rare (and endemic--B. kaiseri), threatened species growing in St. Catherine Protectorate, southern Sinai, Egypt. They are subjected to a number of threats that have caused populations to decline in both number and size. For the long-term survival of these species, an appropriate conservation strategy for the maintenance of their genetic variation should be developed. This study measures genetic diversity within and among populations of these Ballota species and determines the conservation implications of the results. The genetic analyses demonstrated that the three Ballota species maintain relatively high levels of genetic diversity (He = 0.195-0.317) and that most of the their genetic diversity was found within populations (GST = 0.045-0.099). Indirect estimates of historical gene flow for B. undulata and B. saxatilis were relatively high (Nm(W) = 5.25 and 3.37, respectively) but suggest that there is somewhat less gene movement among B. kaiseri populations (Nm(W) = 2.29). The levels of genetic diversity maintained within populations of the three Ballota species indicate that an appropriate sampling design for ex situ safeguarding should capture the majority of the genetic diversity found within these taxa. PMID:16407527
Zaghloul, M S; Hamrick, J L; Moustafa, A A; Kamel, W M; El-Ghareeb, R
In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released\\u000a in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these\\u000a studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze\\u000a these studies.
Mark van de Wouw; Theo van Hintum; Chris Kik; Rob van Treuren; Bert Visser
An emerging concept is that cellular communication in mammals can be mediated by the exchange of genetic information, mainly in the form of microRNAs. This can occur when extracellular vesicles, such as exosomes, secreted by a donor cell are taken up by an acceptor cell. Transfer of genetic material can also occur through intimate membrane contacts between donor and acceptor cells. Specialized cell-cell contacts, such as synapses, have the potential to combine these modes of genetic transfer. PMID:22510790
Mittelbrunn, Maria; Sánchez-Madrid, Francisco
Estimation of genetic diversity of Brassica germplasm provides the basis for rapeseed/mustard genetic improvement. Studies were undertaken to estimate the genetic diversity of 30 lines of Brassica napus using Randomly Amplified Polymorphic DNA (RAPD) primers. A total of 30 B. napus genotypes of local and exotic origin were characterized using molecular markers. Four RAPD primers were used to estimate the genetic distances among the genotypes in all the possible combinations. The genetic diversity study revealed different levels of genetic polymorphism for RAPD primers GLA05, GLA07, GLA09 and GLA 10, resulting in amplification of 5.7, 3.5, 3.1 and 5.4 scorable bands (loci) per genotype, respectively. Individual genetic distances observed among B. napus genotypes ranged from 6.5 to 51%. Bivariate data matrix was generated and genetic distances were calculated using Unweighted Pair Group of Arithmetic Mean (UPGMA) procedure. The UPGMA cluster analyses revealed maximum genetic dissimilarity for 8966-1 and 8969-1 genotypes, closely followed by Ganyou-5, 89127-1, 89111-2 and Mlep-048. It is recommended that among the thirty B. napus genotypes, genetically distinct lines pointed out in the present study, should be used in future breeding programs for improvement of Brassica napus. PMID:19070120
Ahmad, Mian Afaq; Munir, Iqbal; Ali, Waqar; Swati, Zahoor Ahmad; Khattak, Muhammad Saeed; Sohail, Quahir; Khan, Imran
Genetic variation in plants can influence the community structure of associated species, through both direct and indirect interactions. Herbivorous insects are known to feed on a restricted range of plants, and herbivore preference and performance can vary among host plants within a species due to genetically based traits of the plant (e.g., defensive compounds). In a natural system, we expect to find genetic variation within both plant and herbivore communities and we expect this variation to influence species interactions. Using a three-species plant-aphid model system, we investigated the effect of genetic diversity on genetic interactions among the community members. Our system involved a host plant (Hordeum vulgare) that was shared by an aphid (Sitobion avenae) and a hemi-parasitic plant (Rhinanthus minor). We showed that aphids cluster more tightly in a genetically diverse host-plant community than in a genetic monoculture, with host-plant genetic diversity explaining up to 24% of the variation in aphid distribution. This is driven by differing preferences of the aphids to the different plant genotypes and their resulting performance on these plants. Within the two host-plant diversity levels, aphid spatial distribution was influenced by an interaction among the aphid's own genotype, the genotype of a competing aphid, the origin of the parasitic plant population, and the host-plant genotype. Thus, the overall outcome involves both direct (i.e., host plant to aphid) and indirect (i.e., parasitic plant to aphid) interactions across all these species. These results show that a complex genetic environment influences the distribution of herbivores among host plants. Thus, in genetically diverse systems, interspecific genetic interactions between the host plant and herbivore can influence the population dynamics of the system and could also structure local communities. We suggest that direct and indirect genotypic interactions among species can influence community structure and processes.
Zytynska, Sharon E; Frantz, Laurent; Hurst, Ben; Johnson, Andrew; Preziosi, Richard F; Rowntree, Jennifer K
Conscientiousness is an important trait for understanding healthy aging. The present article addresses how behavioral and molecular genetics methodologies can aid in furthering explicating the link between conscientiousness and aspects of health and well-being in later life. We review the etiology of conscientiousness documented by both quantitative and molecular genetics methods. We also discuss the ways behavior genetics can be used to continue to help refine the concept of conscientiousness and to help identify points of etiological overlap between conscientiousness and healthy aging outcomes. Phenotypic research has established nontrivial associations between conscientiousness and important outcomes, but behavior genetic methods can determine what the causal (genetic and environmental) mechanisms are behind these relationships. An empirical example of one of these techniques is provided using twin data from the Midlife in the United States (MIDUS) study. We demonstrate that conscientiousness moderates genetic and environmental influences on problem alcohol use, such that greater levels of conscientiousness buffer against the random effects of the environment. Finally, suggestions for future work in this area are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PMID:23181432
South, Susan C; Krueger, Robert F
The Muslim population of India is known for its historical and socioreligious significance. Literature on the genetic structure of this segment of Indiaâ€™s population is scanty. Therefore we have investigated the allele frequency distribution of haptoglobin (HP) and transferrin (TF) phenotypes among the Muslims to explore the genetic diversity of the Muslim immigrant populations of Aligarh. Aligarh is a city
Riaz Ahmad; Aisha Alam; Farhat Fatima; Absar-ul Hasnain
The paper develops a theoretical framework to explain changes in crop genetic resources. For this purpose the genetic diversity of crop plants is treated as a social\\/natural co-construct of human beings in particular historical settings. To illustrate the potential of such an approach, the history of rapeseed (Brassica rapa L. and Brassica napus L.) breeding in Canada from 1954 to
Arunas Juska; Lawrence Busch; Feng Huang Wu
Differential mortality of cryptic species (i.e., morphologically similar but genetically distinct sibling species) may contribute to observed reductions in genetic diversity at contaminated sites if the members of a complex of cryptic species exhibit differential responses to the contaminants that are present. We conducted toxicity bioassays with both polynuclear aromatic hy- drocarbon and metal contamination on Cletocamptus fourchensisand C. stimpsoni
AXAYACATL ROCHA-OLIVARES; JOHN W. F LEEGER; DAVID W. F OLTZ
A low level of genetic variation in mammalian populations where the census population size is relatively large has been attributed to various factors, such as a naturally small effective population size, historical bottlenecks and social behaviour. The killer whale (Orcinus orca) is an abundant, highly social species with reduced genetic variation. We find no consistent geographical pattern of global diversity
A. Rus Hoelzel; Ada Natoli; Marilyn E. Dahlheim; Carlos Olavarria; Robin W. Baird; Nancy A. Black
Tamarindus indica, commonly called tamarind, is a medium-sized evergreen tree that gives a high yield. The fruit is commonly used as a spice. Despite its commercial importance in the international market, it has been little explored. The genetic diversity and genetic relatedness of 36 tamarind genotypes were studied using amplified fragment length polymorphism (AFLP) markers. Twelve primer pairs were used
Ali Qaid Ahmed Yahya Algabal; Narayanaswamy Papanna; Luke Simon
The role of disturbance in the promotion of biological heterogeneity is widely recognised and occurs at a variety of ecological and evolutionary scales. However, within species, the impact of disturbances that decimate populations are neither predicted nor known to result in conditions that promote genetic diversity. Directly examining the population genetic consequences of catastrophic disturbances however, is rarely possible, as
Jessica Worthington Wilmer; Lynde Murray; Ché Elkin; Chris Wilcox; Darren Niejalke; Hugh Possingham
The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and
S Pérez-Espona; F J Pérez-Barbería; W P Goodall-Copestake; C D Jiggins; I J Gordon; J M Pemberton
The Brassica oilseed crops went through two major breeding bottlenecks during the introgression of genes for zero erucic acid and low glucosinolate content, respectively, which may lead to reduced genetic biodiversity of the crop. This study investigates the impact of these bottlenecks on the genetic diversity within and across European and Chinese winter B. rapa cultivars. We compared eight cultivars
Yong-guo ZHAO; Atta Ofori; Chang-ming LU
The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD), Landrace (CL) and Yorkshire (CY) swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.
Tang, G. Q.; Xue, J.; Lian, M. J.; Yang, R. F.; Liu, T. F.; Zeng, Z. Y.; Jiang, A. A.; Jiang, Y. Z.; Zhu, L.; Bai, L.; Wang, Z.; Li, X. W.
The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhizapolyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines.
Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrao, Ester
This dissertation explores the perceptions and experiences of international students from China and Hong Kong with diversity courses. Using theoretical frameworks that examine the diversity classroom, informal interactional diversity, a diversity typology used to categorize diversity courses, intergroup peer relationships and student…
Daniels, Sonja Gail
There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.
van Zonneveld, Maarten; Scheldeman, Xavier; Escribano, Pilar; Viruel, Maria A.; Van Damme, Patrick; Garcia, Willman; Tapia, Cesar; Romero, Jose; Siguenas, Manuel; Hormaza, Jose I.
More-diverse communities are thought to be ecologically stable because a greater number of ecological interactions among members allows for the increases in robustness and resilience. Diversity–stability relationships have mostly been studied on short ecological time scales but one study has identified such patterns over million-year time scales in reef communities. Here we propose and test a hypothesis for the mechanism of large-scale diversity–stability relationships in reefs. The extinction of community members destabilizes the community as a whole, unless there is sufficient diversity to buffer the community from the stochastic loss of members, thereby preventing collapse. If genera have high extinction rates, any variation in diversity among communities will result in a diversity–stability relationship. Conversely, in the absence of other mechanisms, the stability of low extinction communities is expected to be independent of diversity. We compare the extinction rates of six reef-building metazoan taxa to patterns of reef community stability and reef volume. We find that extinction of reef-builders occurs independent of reef volume, and that the strength of the diversity–stability relationship varies positively with extinction rate.
Simpson, Carl; Kiessling, Wolfgang
Background Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world. Results Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam. Conclusions Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.
Background Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy–body shape, dorsal fin, eye shape, and tailfin–were selected for hypothesis-testing to identify those that better correspond to evolutionary history. Principal Finding Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of FST and Nm revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima’s D and Fu and Li’s D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher’s exact test identified matrilineal constraints on domestication. Conclusions Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy–Grass-goldfish, Egg-goldfish, and Wen-goldfish–better reflected the history of domestication.
Wang, Shu-Yan; Luo, Jing; Murphy, Robert W.; Wu, Shi-Fang; Zhu, Chun-Ling; Gao, Yun; Zhang, Ya-Ping
This qualitative case study explored how families from diverse cultural backgrounds understood family involvement in the context of early childhood care and educational settings. Participants in the study included nine members from six families who had children enrolled in three early childhood care and education programs. The primary method of…
Cardona, Betty; Jain, Sachin; Canfield-Davis, Kathy
Tilman1 has developed a model to predict the number of plant species that can coexist competitively on a limited resource base. Species diversity first increases over low resource supplies, then declines as the environment becomes richer. Although Tilman's model was developed to describe interspecific interactions between plant species, it may also apply to animal species. Tilman1 questions whether animals specialize
Z. Abramsky; M. L. Rosenzweig
Purpose: The purpose of this paper is to investigate the association between employees' perceptions of diversity training (DT) existence and effectiveness with organizational commitment (OC), and career satisfaction (CS). Design/methodology/approach: The analyses in this paper utilize survey data collected between 2006 and 2007 from over 11,000…
Yap, Margaret; Holmes, Mark Robert; Hannan, Charity-Ann; Cukier, Wendy
The cytogenetics of eight Felidae species in Thailand were investigated by the colchicines-hypotonic fixation-air drying technique followed by a conventional technique. All species studied have an identical number of 38 diploid chromosomes, indicating a close genetic relationship among species. At a deep study level, the genetic relationships of eight Felidae species were accessed by the AFLP method. Blood samples were collected from sources locating in their original regions for DNA extraction. With ten successful primer combinations, a total of 4208 scorable bands were generated. Of these bands, 18.91% are polymorphic. Percentages of Polymorphic Bands (PPB) for each primer combination range from 15.00 to 23.59%. The generating bands were used for dendrogram construction. The average genetic similarity values among all Felidae species are 68.20% (between Panthera tigris and Neofelis nebulosa) to 85.53% (between Prionailurus bengalensis and Prionailurus viverrinus). The dendrogram shows that the eight Felidae species were clustered together and the subfamily Pantherinae and Felinae with Neofelis nebulosa are distinguished. The Felinae, Prionailurus bengalensis, Prionailurus viverrinus, Catopuma temminckii, Felis chaus, Pardofelis marmorata and Neofelis nebulosa were clustered together with 91% bootstrap support and the Pantherinae, Panthera pardus is clustered with Panthera tigris with 92% bootstrap support. In summary, the ten successful primer combinations can be used to determine genetic differences among eight Thailand Felidae species. PMID:19070075
Srisamoot, Nattapong; Chaveerach, Arunrat; Nuchadomrong, Suporn; Sattayasai, Nison; Chaveerach, Prapansak; Tanomtong, Alongkoad; Pinthong, Krit
Background Cycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species. Results Analyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna. A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene. Conclusions Some genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively.
Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure\\u000a of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10-bp oligonucleotide primers, which generated 237 RAPD bands,\\u000a were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from\\u000a the east to
J. L. Wang; N. X. Zhao; Y. B. Gai; F. Lin; A. Z. Ren; W. B. Ruan; L. Chen
Background Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.
Silby, Mark W; Cerdeno-Tarraga, Ana M; Vernikos, Georgios S; Giddens, Stephen R; Jackson, Robert W; Preston, Gail M; Zhang, Xue-Xian; Moon, Christina D; Gehrig, Stefanie M; Godfrey, Scott AC; Knight, Christopher G; Malone, Jacob G; Robinson, Zena; Spiers, Andrew J; Harris, Simon; Challis, Gregory L; Yaxley, Alice M; Harris, David; Seeger, Kathy; Murphy, Lee; Rutter, Simon; Squares, Rob; Quail, Michael A; Saunders, Elizabeth; Mavromatis, Konstantinos; Brettin, Thomas S; Bentley, Stephen D; Hothersall, Joanne; Stephens, Elton; Thomas, Christopher M; Parkhill, Julian; Levy, Stuart B; Rainey, Paul B; Thomson, Nicholas R
One of the top-selling medicinal products worldwide is Hypericum perforatum (St. John's Wort). Despite its cosmopolitan distribution and utilization, little is known regarding the relationship of the bioactive compounds in H. perforatum to the plants from which they are purportedly derived. In this study, amplified fragment length polymorphism (AFLP) analysis of 56 Hypericum accessions, representing 11 species, was conducted to gain a better understanding of diversity within Hypericum species, especially within cultivated accessions of H. perforatum, and to establish a molecular methodology that will provide breeders and regulators with a simple, affordable, and accurate tool with which to identify purported H. perforatum material. Utilizing four primer combinations, a total of 298 polymorphic markers were generated, of which 17 were present in all H. perforatum accessions and 2 were specific to only H. perforatum. This study demonstrates that AFLP can be utilized not only to determine the relationships of closely related Hypericum accessions, but as a tool to authenticate material in herbal remedies through the use of genetic fingerprinting.
Percifield, Ryan J.; Hawkins, Jennifer S.; McCoy, Joe-Ann; Widrlechner, Mark P.; Wendel, Jonathan F.
We determined the genetic diversity and evolutionary relationships among 26 Chinese indigenous horse breeds and two introduced horse breeds by genotyping these animals for 27 microsatellite loci. The 26 Chinese horse breeds come from 12 different provinces. Two introduced horse breeds were the Mongolia B Horse from Mongolia and the Thoroughbred Horse from the UK. A total of 330 alleles were detected, and the expected heterozygosity ranged from 0.719 (Elenchuns) to 0.780 (Dali). The mean number of alleles among the horse breeds ranged from 6.74 (Hequ) to 8.81 (Debao). Although there were abundant genetic variations found, the genetic differentiation was low between the Chinese horses, which displayed only 2.4% of the total genetic variance among the different breeds. However, genetic differentiation (pairwise FST) among Chinese horses, although moderate, was still apparent and varied from 0.001 for the Guizou-Luoping pair to 0.064 for the Jingjiang-Elenchuns pair. The genetic differentiation patterns and genetic relationships among Chinese horse breeds were also consistent with their geographical distribution. The Thoroughbred and Mongolia B breeds could be discerned as two distinct breeds, but the Mongolia B horse in particular suffered genetic admixture with Chinese horses. The Chinese breeds could be divided into five major groups, i.e. the south or along the Yangtze river group (Bose, Debao, Wenshan, Lichuan, Jianchang, Guizhou, Luoping, Jinjiang and Dali), the Qinghai-Tibet Plateau group (Chaidamu, Hequ, Datong, Yushu, Tibet Grassland and Tibet Valley), the Northeast of China group (Elenchuns, Jilin and Heihe), the Northwest of China group (Kazakh, Yili and Yanqi) and the Inner Mongolia group (Mongolia A, Sanhe, Xinihe,Wuzhumuqin and Sengeng). This grouping pattern was further supported by principal component analysis and structure analysis. PMID:20477800
Ling, Y H; Ma, Y H; Guan, W J; Cheng, Y J; Wang, Y P; Han, J L; Mang, L; Zhao, Q J; He, X H; Pu, Y B; Fu, B L
Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers. PMID:24499432
Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A
The genus Theobroma, recently reclassified in the family Malvaceae, comprises some species with high economic potential, including the cupuí, Theobroma subincanum Mart., which has not yet been domesticated, and whose genetics and population structure are mostly unknown. This study aimed to assess the population structure and genetic diversity in natural populations of T. subincanum Mart., using inter-simple sequence repeat (ISSR) markers. A total of 59 individuals were sampled in three geographically separate populations, CFA, CMN, and CPT. Nei's genetic distance was estimated to characterize populations with the use of 13 polymorphic primers. The analysis of molecular variance revealed that the variability between populations (51.71%) was higher than that within populations (48.29%). Among the three populations, CPT showed the highest diversity index and percentage of polymorphism. The ISSR molecular markers were efficient and presented sufficient polymorphism to estimate genetic diversity in populations of T. subincanum Mart. PMID:24301761
Rivas, L H; Giustina, L D; Luz, L N; Karsburg, I V; Pereira, T N S; Rossi, A A B
Genetic diversity and relationships in 74 Helicobacter pylori isolates recovered from patients assigned to distinct clinical categories were estimated by examination of allelic variation in six genes encoding metabolic housekeeping enzymes by multilocus enzyme electrophoresis. Seventy-three distinct allele profiles, representing multilocus chromosomal genotypes, were identified. All six loci were highly polymorphic, with an average of 11.2 alleles per locus. The mean genetic diversity in the sample was 0.735, a value that exceeds the level of diversity recorded in virtually all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles (lack of enzyme activity) was identified and warrants further investigation at the molecular level. Lack of linkage disequilibrium (nonrandom association (of alleles over loci) indicates that horizontal transfer and recombination of metabolic enzyme genes have contributed to the generation of chromosomal diversity in H. pylori. In this sample of isolates, there was no statistically significant association of multilocus enzyme electrophoretic types or cluster of related chromosomal types and disease category.
Go, M F; Kapur, V; Graham, D Y; Musser, J M
The Japanese crested ibis Nipponia nippon is a critically threatened bird. We assessed genetic diversity and structure in the Sado captive population of the Japanese crested ibis based on 24 and 50 microsatellite markers developed respectively for the same and related species. Of a total of 74 loci, 19 showed polymorphisms in the five founder birds of the population, and therefore were useful for the analysis of genetic diversity and structure. Genetic diversity measures, A, ne, He, Hoand PIC, obtained by genotyping of the 138 descendants were similar to those of other species with population bottlenecks, and thus considerably low. The low level of genetic diversity resulting from such bottlenecks was consistent with the results of lower genetic diversity measures for the Sado captive relative to the Chinese population that is the source population for the Sado group as determined using previously reported data and heterozygosity excess by Hardy-Weinberg equilibrium tests. Further, individual clustering based on the allele-sharing distance and Bayesian model-based clustering revealed that the founder genomes were equally at population in total, and with various admixture patterns at individual levels inherited by the descendants. The clustering results, together with the result of inheritance of all alleles of the microsatellites from the founders to descendants, suggest that planned mating in captive-breeding programs for the population has succeeded in maintaining genetic diversity and minimizing kinship. In addition, the Bayesian model-based clustering assumed two different components of genomes in the Sado captive Japanese crested ibis, supporting a considerably low level of genetic diversity. PMID:23721466
Urano, Kensuke; Tsubono, Kanako; Taniguchi, Yukio; Matsuda, Hirokazu; Yamada, Takahisa; Sugiyama, Toshie; Homma, Kosuke; Kaneko, Yoshinori; Yamagishi, Satoshi; Iwaisaki, Hiroaki
Background Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. Results According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification. Conclusions A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.
The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (FST?=?0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (FST?=?0.116, Nm?=?1.89) than those in the eastern group (FST?=?0.049, Nm?=?4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r?=?0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.
Duan, Yun; Wu, Yu-qing; Luo, Li-zhi; Miao, Jin; Gong, Zhong-jun; Jiang, Yue-li; Li, Tong
BIOLOGICAL diversity, population size and body size are interde-pendent1-8, but there is little consensus on the nature or causes of these relations. Here we analyse the most thoroughly sampled ecological community to date, a grassland insect community sample containing 89,596 individuals of 1,167 species. Each taxonomic order had a distinct body size at which both species richness and number of
Evan Siemann; David Tilman; John Haarstad
The impact of antiretroviral therapy (ART) on the genetics of simian immunodeficiency virus (SIV) or human immunodeficiency virus (HIV) populations has been incompletely characterized. We analyzed SIV genetic variation before, during, and after ART in a macaque model. Six pigtail macaques were infected with an SIV/HIV chimeric virus, RT-SHIV(mne), in which SIV reverse transcriptase (RT) was replaced by HIV-1 RT. Three animals received a short course of efavirenz (EFV) monotherapy before combination ART was started. All macaques received 20 weeks of tenofovir, emtricitabine, and EFV. Plasma virus populations were analyzed by single-genome sequencing. Population diversity was measured by average pairwise difference, and changes in viral genetics were assessed by phylogenetic and panmixia analyses. After 20 weeks of ART, viral diversity was not different from pretherapy viral diversity despite more than 10,000-fold declines in viremia, indicating that, within this range, there is no relationship between diversity and plasma viremia. In two animals with consistent SIV RNA suppression to <15 copies/ml during ART, there was no evidence of viral evolution. In contrast, in the four macaques with viremias >15 copies/ml during therapy, there was divergence between pre- and during-ART virus populations. Drug resistance mutations emerged in two of these four animals, resulting in virologic failure in the animal with the highest level of pretherapy viremia. Taken together, these findings indicate that viral diversity does not decrease with suppressive ART, that ongoing replication occurs with viremias >15 copies/ml, and that in this macaque model of ART drug resistance likely emerges as a result of incomplete suppression and preexisting drug resistance mutations. PMID:21084490
Kearney, Mary; Spindler, Jon; Shao, Wei; Maldarelli, Frank; Palmer, Sarah; Hu, Shiu-Lok; Lifson, Jeffrey D; KewalRamani, Vineet N; Mellors, John W; Coffin, John M; Ambrose, Zandrea
The level of genetic diversity of aquatic species is a critical indicator of stream system condition for which few data exist. There is strong evidence suggesting that environmental stressors affect the genetic diversity of exposed populations. In order to study genetic diversi...
Nucleotide sequences were determined for the complete M genome segments of two distinct hantavirus genetic lineages which were detected in hantavirus antibody- and PCR-positive white-footed mice (Peromyscus leucopus) from Indiana and Oklahoma. Phylogenetic analyses indicated that although divergent from each other, the virus lineages in Indiana and Oklahoma were monophyletic and formed a newly identified unique ancestral branch within the clade of Sin Nombre-like viruses found in Peromyscus mice. Interestingly, P. leucopus-borne New York virus was found to be most closely related to the P. maniculatus-borne viruses, Sin Nombre and Monongahela, and monophyletic with Monongahela virus. In parallel, intraspecific phylogenetic relationships of P. leucopus were also determined, based on the amplification, sequencing, and analysis of the DNA fragment representing the replication control region of the rodent mitochondrial genome. P. leucopus mitochondrial DNA haplotypes were found to form four separate genetic clades, referred to here as Eastern, Central, Northwestern, and Southwestern groups. The distinct Indiana and Oklahoma virus lineages were detected in P. leucopus of the Eastern and Southwestern mitochondrial DNA haplotypes, respectively. Taken together, our current data suggests that both cospeciation of Peromyscus-borne hantaviruses with their specific rodent hosts and biogeographic factors (such as allopatric migrations, geographic separation, and isolation) have played important roles in establishment of the current genetic diversity and geographic distribution of Sin Nombre-like hantaviruses. In particular, the unusual position of New York virus on the virus phylogenetic tree is most consistent with an historically recent host-switching event. PMID:9420200
Morzunov, S P; Rowe, J E; Ksiazek, T G; Peters, C J; St Jeor, S C; Nichol, S T
Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico. PMID:19495796
Sandoval, Karla; Buentello-Malo, Leonor; Peñaloza-Espinosa, Rosenda; Avelino, Heriberto; Salas, Antonio; Calafell, Francesc; Comas, David
Disturbance is a key factor shaping species abundance and diversity in plant communities. Here, we use a mechanistic model of vegetation diversity to show that different strengths of r- and K-selection result in different disturbance-diversity relationships. R- and K-selection constrain the range of viable species through the colonization-competition tradeoff, with strong r-selection favoring colonizers and strong K-selection favoring competitors, but the level of disturbance also affects the success of species. This interplay among r- and K-selection and disturbance results in different shapes of disturbance-diversity relationships, with little variation of diversity with no r- and no K-selection, a decrease in diversity with r-selection with disturbance rate, an increase in diversity with K-selection, and a peak at intermediate values with strong r- and K-selection. We conclude that different disturbance-diversity relationships found in observations may reflect different intensities of r- and K-selection within communities, which should be inferable from broader observations of community composition and their ecophysiological trait ranges.
Bohn, Kristin; Pavlick, Ryan; Reu, Bjorn; Kleidon, Axel
The popularity of genetically modified insect resistant (Bt) cotton has promoted large scale monocultures, which is thought to worsen the problem of crop genetic homogeneity. Information on genetic diversity among Bt cotton varieties is lacking. We evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. Thirty-seven of 104 surveyed primers were found informative. Fifty-two primers selected on the basis of reported intra-hirsutum polymorphism in a cotton marker database showed a high degree of polymorphism, 56% compared to 13% for randomly selected primers. A total of 177 loci were amplified, with an average of 1.57 loci per primer, generating 38 markers. The amplicons ranged in size from 98 to 256 bp. The genetic similarities among the 19 genotypes ranged from 0.902 to 0.982, with an average of 0.947, revealing a lack of diversity. Similarities among genotypes from public sector organizations were higher than genotypes developed by private companies. Hybrids were found to be more distant compared to commercial cultivars and advanced breeding lines. Cluster analysis grouped the 19 Bt cotton genotypes into three major clusters and two independent entries. Cultivars IR-3701, Ali Akbar-802 and advanced breeding line VH-259 grouped in subcluster B2, with very narrow genetic distances despite dissimilar parentage. We found a very high level of similarity among Pakistani-bred Bt cotton varieties, which means that genetically diverse recurrent parents should be included to enhance genetic diversity. The intra-hirsutum polymorphic SSRs were found to be highly informative for molecular genetic diversity studies in these cotton varieties. PMID:22535395
Ullah, I; Iram, A; Iqbal, M Z; Nawaz, M; Hasni, S M; Jamil, S
Melioidosis is caused by the gram-negative saprophytic bacterium Burkholderia pseudomallei, which is endemic to southeast Asia and northern Australia. We have previously found evidence of geographic localization of strains based on multilocus sequence typing (MLST). In this study, we examined the diversity of 277 isolates from northern Australia, which were resolved into 159 different sequence types. No sequence types were common to both Queensland and the Northern Territory, and there was significant differentiation between the alleles present in the two regions. The considerable diversity in sequence types contrasts with the limited diversity of alleles at MLST loci, supporting previous work suggesting a high rate of recombination relative to mutation in B. pseudomallei, where new sequence types are primarily generated by reassortment of existing alleles.
Cheng, Allen C.; Ward, Linda; Godoy, Daniel; Norton, Robert; Mayo, Mark; Gal, Daniel; Spratt, Brian G.; Currie, Bart J.
In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity. PMID:20054521
van de Wouw, Mark; van Hintum, Theo; Kik, Chris; van Treuren, Rob; Visser, Bert
We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology.
Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.
Although previous literature has demonstrated the importance of age, ethnicity, and socioeconomic status in understanding grandparent–grandchild relationships, additional factors contribute to a more complete and nuanced understanding of multigenerational relationships. Thorough understanding of the role of diversity requires examination of the discrete impacts of grandparents’ gender, sexual orientation, and physical and/or cognitive limitations on the relationship. This article focuses on these 3 important, yet overlooked, issues of diversity, with a focus on strength-based and empowerment-oriented strategies and their implications for practice, policy, and future research.
Stelle, Charlie; Fruhauf, Christine A.; Orel, Nancy; Landry-Meyer, Laura
Background Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift. Results Genetic differentiation (FST) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically. Conclusions Compared to other vent species, DNA sequence diversity is extremely low in R. pachyptila. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events.
The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is 10 times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple timescales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as an outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neutral sites is U shaped, which is a characteristic feature of pervasive linked selection. Based on the additional findings (i) that the majority of nonsynonymous variation is eliminated over timescales on the order of the separation between clades, (ii) that diversity is reduced in gene-rich regions, and (iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus. PMID:24443445
Rödelsperger, Christian; Neher, Richard A; Weller, Andreas M; Eberhardt, Gabi; Witte, Hanh; Mayer, Werner E; Dieterich, Christoph; Sommer, Ralf J
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 five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.
Liu, Kejun; Goodman, Major; Muse, Spencer; Smith, J Stephen; Buckler, Ed; Doebley, John
Aims We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1) determine the level of genetic diversity across the studied regions; (2) explore the likely origins of invasive populations in China; and (3) investigate whether there is the evidence of multiple introductions into China. Methods We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China. Important Findings We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (FIS) or population differentiation (FST). Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.
Zhao, Jiali; Solis-Montero, Lislie; Lou, Anru; Vallejo-Marin, Mario
Background Febrile respiratory illness (FRI) has a high impact on public health and global economics and poses a difficult challenge for differential diagnosis. A particular issue is the detection of genetically diverse pathogens, i.e. human rhinoviruses (HRV) and enteroviruses (HEV) which are frequent causes of FRI. Resequencing Pathogen Microarray technology has demonstrated potential for differential diagnosis of several respiratory pathogens simultaneously, but a high confidence design method to select probes for genetically diverse viruses is lacking. Results Using HRV and HEV as test cases, we assess a general design strategy for detecting and serotyping genetically diverse viruses. A minimal number of probe sequences (26 for HRV and 13 for HEV), which were potentially capable of detecting all serotypes of HRV and HEV, were determined and implemented on the Resequencing Pathogen Microarray RPM-Flu v.30/31 (Tessarae RPM-Flu). The specificities of designed probes were validated using 34 HRV and 28 HEV strains. All strains were successfully detected and identified at least to species level. 33 HRV strains and 16 HEV strains could be further differentiated to serotype level. Conclusion This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.
Wang, Zheng; Malanoski, Anthony P; Lin, Baochuan; Kidd, Carolyn; Long, Nina C; Blaney, Kate M; Thach, Dzung C; Tibbetts, Clark; Stenger, David A
Climate change has the potential to alter the genetic diversity of plant populations with consequences for community dynamics and ecosystem processes. Recent research focused on changes in climatic means has found evidence of decreased precipitation amounts reducing genetic diversity. However, increased variability in climatic regimes is also predicted with climate change, but the effects of this aspect of climate change on genetic diversity have yet to be investigated. After 10 years of experimentally increased intra-annual variability in growing season precipitation regimes, we report that the number of genotypes of the dominant C(4) grass, Andropogon gerardii Vitman, has been significantly reduced in native tallgrass prairie compared with unmanipulated prairie. However, individuals showed a different pattern of genomic similarity with increased precipitation variability resulting in greater genome dissimilarity among individuals when compared to unmanipulated prairie. Further, we found that genomic dissimilarity was positively correlated with aboveground productivity in this system. The increased genomic dissimilarity among individuals in the altered treatment alongside evidence for a positive correlation of genomic dissimilarity with phenotypic variation suggests ecological sorting of genotypes may be occurring via niche differentiation. Overall, we found effects of more variable precipitation regimes on population-level genetic diversity were complex, emphasizing the need to look beyond genotype numbers for understanding the impacts of climate change on genetic diversity. Recognition that future climate change may alter aspects of genetic diversity in different ways suggests possible mechanisms by which plant populations may be able to retain a diversity of traits in the face of declining biodiversity. PMID:22907523
Avolio, Meghan L; Beaulieu, Jeremy M; Smith, Melinda D
Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the invasive success of P. cespitosum in its introduced range. PMID:24695495
Matesanz, Silvia; Theiss, Kathryn E; Holsinger, Kent E; Sultan, Sonia E
Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America), via the analyses of 516 individuals, and asked the following questions: 1) Do populations have differing levels of within-population genetic diversity? 2) Do populations form distinct genetic clusters? 3) Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering) and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources) in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further contribute to the invasive success of P. cespitosum in its introduced range.
Matesanz, Silvia; Theiss, Kathryn E.; Holsinger, Kent E.; Sultan, Sonia E.