共查询到20条相似文献,搜索用时 31 毫秒
1.
In order to investigate the mechanisms creating and maintaining variability at the major histocompatibility (MH) class II alpha (DAA) locus we examined patterns of polymorphism in two isolated Atlantic salmon populations which share a common post-glacial origin. As expected from their common origin, but contrary to the observation at the MH class I locus, these populations shared the majority of DAA alleles: out of 17 sequences observed, 11 were common to both populations. Recombination seems to play a more important role in the origin of new alleles at the class II alpha locus than at the class I locus. A greater than expected proportion of sites inferred to be positively selected (potentially peptide binding residues, PBRs) were found to be involved in recombination events, suggesting a mechanism for increasing MH variability through an interaction between recombination and natural selection. Thus it appears that although selection and recombination are important mechanisms for the evolution of both class II alpha and class I loci in the Atlantic salmon, the pattern of variability differs markedly between these classes of MH loci. 相似文献
2.
Joëlle Goüy de Bellocq Franz Suchentrunk Stuart J. E. Baird Helmut Schaschl 《Immunogenetics》2009,61(2):131-144
We surveyed the genetic diversity of the expressed major histocompatibility complex class II DQA locus in natural populations
of European brown hares, Lepus europaeus, from Austria and Belgium (267 individuals in total). Based on cDNA sequences, we designed hare-specific primers to amplify
the highly variable second exon of the DQA gene. Using cloning–sequencing methodology and capillary electrophoresis single-strand
conformation polymorphism, we found ten alleles of the DQA exon 2 locus across these two European regions, of which eight
are described for the first time. To search for signals of selection and recombination in the evolution of the DQA gene within
the leporids, we augmented our sample with orthologous DQA alleles from the European rabbit, Oryctolagus cuniculus, in order to carry out a species level, species pairwise comparison. We found evidence of recombination in the history of
the DQA sequences in leporids with some recombinant alleles bridging the species divide. In both species, selection on peptide
binding site codons can be detected, though stronger for the rabbit. This result suggests that there may be a differential
selection pressure in the deeper evolutionary history of these two species due to differences in several demographic and ecological
traits likely subjecting them to differential selection by parasites. Finally, evolutionary relationships show a widespread
and statistically significant intermingling of alleles from the two species. The many macroparasites shared between hares
and rabbits may explain this pattern of trans-species polymorphism.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The nucleotide sequence data reported in this paper have been submitted to Genbank and have been assigned the accession numbers
FJ225335–FJ225346. 相似文献
3.
Correlation between body length and characteristics of genetic polymorphism for loci Me-2, IDHP-3, ESTD-1, and AAT-2 were studied in the Atlantic salmon Salmo salar. The study was based on data on genetic variation in more than 4000 fish grown at the Kandalaksha Hatchery. Of four loci studied, loci ESTD-1 and IDHP-3 were distinguished by the fact that they can be confidently considered body-length markers in the Atlantic salmon. Analysis of mean locus heterozygosity indicates a disturbance of the mechanism of negative heterosis that is characteristic of natural populations. This presumably reflects a change in the genetic diversity of the Atlantic salmon under the influence of breeding. 相似文献
4.
Jeremiah W. Busch Simon Joly Daniel J. Schoen 《Evolution; international journal of organic evolution》2010,64(6):1657-1670
Genetic diversity at the S‐locus controlling self‐incompatibility (SI) is often high because of negative frequency‐dependent selection. In species with highly patchy spatial distributions, genetic drift can overwhelm balancing selection and cause stochastic loss of S‐alleles. Natural selection may favor the breakdown of SI in populations with few S‐alleles because low S‐allele diversity constrains the seed production of self‐incompatible plants. We estimated S‐allele diversity, effective population sizes, and migration rates in Leavenworthia alabamica, a self‐incompatible mustard species restricted to discrete habitat patches in rocky glades. Patterns of polymorphism were investigated at the S‐locus and 15 neutral microsatellites in three large and three small populations with 100‐fold variation in glade size. Populations on larger glades maintained more S‐alleles, but all populations were estimated to harbor at least 20 S‐alleles, and mate availabilities typically exceeded 0.80, which is consistent with little mate limitation in nature. Estimates of the effective size (Ne) in each population ranged from 600 to 1600, and estimated rates of migration (m) ranged from 3 × 10−4 to nearly 1 × 10−3. According to theoretical models, there is limited opportunity for genetic drift to reduce S‐allele diversity in populations with these attributes. Although pollinators or resources limit seed production in small glades, limited S‐allele diversity does not appear to be a factor promoting the incipient breakdown of SI in populations of this species that were studied. 相似文献
5.
Joëlle Goüy de Bellocq Christiane Delarbre Gabriel Gachelin Serge Morand 《Global Ecology and Biogeography》2005,14(2):115-122
Aim Polymorphism at neutral markers and at MHC loci in rodent populations living on islands is generally low. The main genetic factors that may contribute to a reduced level of genetic variability are genetic drift, reduced gene flow and founder events. We investigated the pattern of polymorphism at the second exon of the Mhc‐DQA gene in island populations of Apodemus sylvaticus and in their mainland counterparts to investigate the pattern of MHC polymorphism in a phylogeographical context and to assess the impact of insularity on diversity at this locus. Location Eight north Mediterranean populations of Apodemus sylvaticus were studied, including five island populations (Majorca, Minorca, Porquerolles, Port‐Cros and Sicily) and three mainland populations. Methods cDNA sequencing and nucleotide sequences analyses. Synonymous and non‐synonymous substitutions were examined at the PBR and non‐PBR sites. The DQA allelic distribution in populations was compared with the woodmouse phylogeography. Results This study presents novel DQA alleles. High polymorphism of the DQA locus is recorded in natural populations of A. sylvaticus with 13 alleles being widely distributed irrespective of the geographical origin and palaeoclimatic history of populations. The DQA locus does not show the expected pattern for non‐synonymous substitutions at the PBR sites. However, island populations show a weak loss of polymorphism in comparison with their mainland counterparts. Main conclusions The DQA locus in the woodmouse seems to be subject to weak selection and does not allow resolution of phylogeographical relationships among European woodmouse populations. The presence of at least three alleles in island populations and the maintenance of five alleles between the two European lineages over 1.5 Myr suggest that balancing selection may act within populations, and more precisely within island populations, to maintain genetic variability. This study shows that phylogeographical studies are a prerequisite for any genetic investigation of selected genes in natural populations. 相似文献
6.
Elizabeth A. Archie Tammy Henry Jesus E. Maldonado Cynthia J. Moss Joyce H. Poole Virginia R. Pearson Suzan Murray Susan C. Alberts Robert C. Fleischer 《Immunogenetics》2010,62(2):85-100
Genes of the vertebrate major histocompatibility complex (MHC) are crucial to defense against infectious disease, provide
an important measure of functional genetic diversity, and have been implicated in mate choice and kin recognition. As a result,
MHC loci have been characterized for a number of vertebrate species, especially mammals; however, elephants are a notable
exception. Our study is the first to characterize patterns of genetic diversity and natural selection in the elephant MHC.
We did so using DNA sequences from a single, expressed DQA locus in elephants. We characterized six alleles in 30 African
elephants (Loxodonta africana) and four alleles in three Asian elephants (Elephas maximus). In addition, for two of the African alleles and three of the Asian alleles, we characterized complete coding sequences
(exons 1–5) and nearly complete non-coding sequences (introns 2–4) for the class II DQA loci. Compared to DQA in other wild
mammals, we found moderate polymorphism and allelic diversity and similar patterns of selection; patterns of non-synonymous
and synonymous substitutions were consistent with balancing selection acting on the peptides involved in antigen binding in
the second exon. In addition, balancing selection has led to strong trans-species allelism that has maintained multiple allelic
lineages across both genera of extant elephants for at least 6 million years. We discuss our results in the context of MHC
diversity in other mammals and patterns of evolution in elephants. 相似文献
7.
The colonial urochordate Botryllus schlosseri is a sedentary species of Mediterranean origin that became cosmopolitan, probably because of postglacial-period dispersal
and human-mediated invasions of colonies attached to ship hulls. Here we studied microsatellite allele diversity of Atlantic
coast populations from an area ranging from European regions south of the last glacial front to regions that had been permanently
ice-covered. Gene diversity levels varied dramatically among populations residing in areas subject to different glacial conditions.
Five populations from the Iberian Peninsula, in an area south of the last glacial front, as well as two populations from presumed
refugia in Brittany, expressed high gene diversity values (expected heterozygosity [He]: 0.76–0.80; average number of alleles
per locus [A]: 7.25–8.75). Two populations inhabiting areas that experienced permafrost conditions (Helgoland Island, Germany,
and Plymouth, England) had intermediate values (He: 0.40–0.42; A: 3.0–4.0), whereas the Auchenmalg, Scotland, population,
from an area previously covered by ice, showed a remarkably low value (He: 0.17; A: 1.75). Therefore, most European populations
of B. schlosseri mirrored the movement of the ice front in the last ice age. A second population from the area that was covered by permanent
ice (Lossiemouth, Scotland), however, had a high He of 0.61 and an intermediate A of 3.67. Results were compared with recent
invasions (populations less than 200 years old) in the United States and New Zealand that had a higher degree of genetic variation
than the European native populations established thousands of years ago. Given the overall dearth of studies on this subject,
we suggest that in contemporary established Botryllus populations, gene diversity is affected by ecological factors, some of which can be traced directly to the last ice age.
Other parameters of gene diversity are influenced by selection pressure, which might be more intense in northern regions. 相似文献
8.
Junco Nagata Youichi Sonoda Keiko Hamaguchi Naoki Ohnishi Soh Kobayashi Ken Sugimura Fumio Yamada 《Conservation Genetics》2009,10(4):1121-1123
We report on the isolation and characterization of eight polymorphic and five monomorphic microsatellites in the Amami rabbit
(Pentalagus furnessi). Microsatellite polymorphism was determined using 25 individuals. There were 2–11 alleles for each polymorphic locus with
heterozygosity ranging between 0.08 and 0.76. Linkage disequilibrium was not suggested between any pairs among the eight polymorphic
loci. We suggest that these primers be used in future studies to monitor population size, determine dispersal patterns, and
genetic diversity within and between populations of this and related species. 相似文献
9.
Analysis of caprine pituitary specific transcription factor-1 gene polymorphism in indigenous Chinese goats 总被引:1,自引:0,他引:1
Lan XY Li MJ Chen H Zhang LZ Jing YJ Wei TB Ren G Wang X Fang XT Zhang CL Lei CZ 《Molecular biology reports》2009,36(4):705-709
Since mutations on POU1F1 gene possibly resulted in deficiency of GH, PRL, TSH and POU1F1, this study revealed the polymorphism of goat POU1F1-AluI locus and analyzed the distribution of alleles on 13 indigenous Chinese goat breeds. The PCR-RFLP analysis showed the predominance
of TT genotype and the frequencies of allele T varied from 0.757 to 0.976 in the analyzed populations (SBWC, Bo, XH and HM).
Further study, distributions of genotypic and allelic frequencies at this locus were found to be significantly different among
populations based on a χ2-test (P < 0.001), suggesting that the breed factor significantly affected the molecular genetic character of POU1F1 gene. The genetic diversity analysis revealed that Chinese indigenous populations had a wide spectrum of genetic diversity
in goat POU1F1-AluI locus. However, the ANOVA analysis revealed no significant differences for gene homozygosty, gene heterozygosty, effective
allele numbers and PIC (polymorphism information content) among meat, dairy and cashmere utility types (P > 0.05), suggesting that goat utility types had no significant effect on the spectrum of genetic diversity.
X. Y. Lan and M. J. Li equally contributed to this work. 相似文献
10.
Paula Feliciano de Lima Flávio Nunes Ramos Maria Imaculada Zucchi Milene Möller Regina Helena Geribello Priolli Carlos Augusto Colombo Vera Nisaka Solferini 《Conservation Genetics》2009,10(6):1883-1886
The shrub species Psychotria tenuinervis (Rubiaceae) is native to the Brazilian Atlantic forest and is largely found within natural and disturbed forest fragments.
Aiming to develop studies on population genetic structure of forest fragment species, eigth microsatellite markers were developed
for P. tenuinervis. Also, 15 loci already developed for Coffea (Rubiaceae) were tested for transferability to this species. We utilized 45 individuals from natural populations of three
different fragments-anthropic edge, interior fragment and natural edge, within the Brazilian Atlantic forest. The average
number of alleles per locus was 2.5 (two–four alleles/locus). These loci will be useful for future population genetic studies
aiming to the conservation and management of this species. 相似文献
11.
High levels of genetic divergence and inbreeding in populations of cupuassu (Theobroma grandiflorum)
Rafael M. Alves Alexandre M. Sebbenn Angela S. Artero Charles Clement Antonio Figueira 《Tree Genetics & Genomes》2007,3(4):289-298
Theobroma grandiflorum (cupuassu) is an important fruit tree native to the Brazilian Amazon. Establishing the genetic diversity and structure of
populations is critical to define long-term strategies for cupuassu conservation presently threatened by rapid deforestation.
Three natural populations collected at the putative center of diversity, three groups of accessions established at a germplasm
collection, and one derived from commercial plantings were analyzed. The genetic diversity was assessed using 21 polymorphic
microsatellite loci originally developed for Theobroma cacao, disclosing a total of 113 alleles. The estimated genetic diversity parameters averaged over cupuassu populations (A = 3.53 alleles per locus; H
e = 0.426; H
o = 0.346) were lower than the values reported for other Neotropical tree species. The three natural populations presented
a positive and significant fixation index (f), ranging from 0.133 to 0.234. Cupuassu apparently adhered to a general pattern of genetic diversity structure of some Neotropical
tree species occurring at low densities, with a low intrapopulation genetic diversity and important levels of endogamy, possibly
due to biparental inbreeding derived from the presence of spatial genetic structure in the populations. A high level of genetic
divergence was detected among the natural populations (θ
p = 0.301), a strong differentiation caused by limited gene flow, and suggesting that human interference in spreading and/or
stimulating plantings might have had a smaller effect than expected. The approximate location of the T. grandiflorum center of diversity could not be confirmed by analyzing natural populations from the putative region. 相似文献
12.
Robert Bernatzky 《Biochemical genetics》1993,31(3-4):173-184
Phenotypic diversity of self-incompatibility (S) alleles within nine natural populations ofLycopersicon peruvianum was investigated. Only 7 incompatible responses were observed of a total of 276 unique combinations tested, on the basis
of controlled pollinations, indicating the large number of alleles that exist within these populations. Molecular weight polymorphism
for specific major stylar proteins observed on SDS-PAGE was also evident in two of the populations examined. Five proteins
were shown to map to theS locus and to be associated with differentS alleles through controlled pollinations and segregation of the proteins. Two of theseS related proteins had been described previously in terms of spatial and temporal expression consistent with their involvement
in self-incompatibility (Mauet al., Planta
169, 184–191, 1986). A mapping population derived from a fully compatible cross was used to establish linkage of theS locus to two DNA markers,CD15 andTG184, that lie on chromosome 1. The order of the markers and estimates of map distances are given. 相似文献
13.
Sílvia S. Monteiro José V. Vingada Alfredo López Graham J. Pierce Marisa Ferreira Andrew Brownlow 《Marine Biology Research》2016,12(6):595-607
Determining how intra-specific genetic diversity is apportioned among natural populations is essential for detecting local adaptation and identifying populations with inherently low levels of extant diversity which may become a conservation concern. Sequence polymorphism at two adaptive loci (MHC DRA and DQB) was investigated in long-finned pilot whales (Globicephala melas) from four regions in the North Atlantic and compared with previous data from New Zealand (South Pacific). Three alleles were resolved at each locus, with trans-species allele sharing and higher levels of non-synonymous to synonymous substitution, especially in the DQB locus. Overall nucleotide diversities of 0.49?±?0.38% and 4.60?±?2.39% were identified for the DRA and DQB loci, respectively, which are relatively low for MHC loci in the North Atlantic, but comparable to levels previously described in New Zealand (South Pacific). There were significant differences in allele frequencies within the North Atlantic and between the North Atlantic and New Zealand. Patterns of diversity and divergence are consistent with the long-term effects of balancing selection operating on the MHC loci, potentially mediated through the effects of host-parasite coevolution. Differences in allele frequency may reflect variation in pathogen communities, coupled with the effects of differential drift and gene flow. 相似文献
14.
K. L. Ciborowski S. Consuegra C. García de Leániz J. Wang M. A. Beaumont W. C. Jordan 《Conservation Genetics》2007,8(6):1355-1367
Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European
origin during the period 1974–1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from
1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect
variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking,
haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency
of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to
those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before
stocking (1950s/1960s Φ
ST = –0.00296–0.00284), increasing considerably at the height of stocking (1980s Φ
ST = 0.18932) and decreasing post-stocking (1990s/2002 Φ
ST = 0.04934–0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability.
Additionally, we found significant differentiation between individuals that had probably died from infectious disease and
apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results
suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population
declines. 相似文献
15.
Many animal populations that are endangered in mainland areas exist in stable island populations, which have the potential
to act as an “ark” in case of mainland population declines. Previous studies have found neutral genetic variation in such
species to be up to an order of magnitude lower in island compared to mainland populations. If low genetic variation is prevalent
across fitness-related loci, this would reduce the effectiveness of island populations as a source of individuals to supplement
declining mainland populations or re-establish extinct mainland populations. One such species, the black-footed rock-wallaby
(Petrogale lateralis lateralis), exists within fragmented mainland populations and small island populations off Western Australia. We examined sequence
variation in this species within a fitness-related locus under positive selection, the MHC class II DAB β1 locus. The mainland populations displayed greater levels of allelic diversity (4–7 alleles) than the island population,
despite being small and isolated, and contained at least two DAB gene copies. The island population displayed low allelic diversity (2 alleles) and fewer alleles per individual in comparison
to mainland populations, and probably possesses only one DAB gene copy. The patterns of DAB diversity suggested that the island population has a markedly lower level of genetic variation than the mainland populations,
in concordance with results from microsatellites (genotyped in a previous study), but preserved unique alleles which were
not found in mainland populations. Where possible, conservation actions should pool individuals from multiple populations,
not only island populations, for translocation programs, and focus on preventing further declines in mainland populations. 相似文献
16.
Codonopsis pilosula Nannf., as an important traditional Chinese medicinal plant species, has been used to treat fatigue, thirst and loss of appetite.
In this study, we developed 10 new microsatellite loci primers from the genome of this species using the combined biotin capture
method. The polymorphism of each locus was further assessed through 27 individuals from four geographically distant populations.
The number of alleles per locus ranged from 6 to 11. The observed and expected heterozygosity ranged from 0.15 to 0.24 and
0.27 to 0.40, respectively. We further performed cross-priming tests of these loci in the other three congeneric species.
These microsatellite markers will be useful for investigating genetic diversity within and between populations of these species. 相似文献
17.
Theresa R. Pope 《International journal of primatology》1998,19(1):95-109
The muriqui or woolly spider monkey (Brachyteles arachnoids) is an endangered primate endemic to the Atlantic Forest of Brazil, <5% of which remains. The known muriqui population consists of <700 individuals separated into approximately 15 geographically isolated forest fragments. I present data on the distribution of genetic variation within and between two such remnant populations (FE and FBR) and summarize the implications of these results for long-range management of species genetic diversity. Eleven of 32 allozyme loci were polymorphic, representing an overall level of polymorphism of 34.4% and a mean heterozygosity per locus of 11%. Both values are among the highest reported for New World monkeys. Genetic differentiation between the two localities is highly significant (FST = 0.413, p < 0.001). Genetic distance between them is an order of magnitude greater than that between other populations of platyrrhine subspecies, but this could be an artifact of the small sample size from FBR. High levels of genetic diversity apparently characteristic of this species persist because (1) fragmentation and size reduction of muriqui populations has occurred very rapidly relative to the muriqui life span—although both polymorphism and heterozygosity were lost between generations in the largest population, the high genetic diversity present in the parent population was still in evidence; and (2) genetic diversity before population fragmentation by human activity was not distributed uniformly throughout the species' historic distribution. Thus, remnant muriqui populations are important genetic reservoirs of alleles that are unique or rare in the species gene pool as a whole. These results emphasize the need for the integration of conservation management efforts throughout the species range. 相似文献
18.
Restriction fragment length polymorphism diversity in soybean 总被引:7,自引:0,他引:7
P. Keim R. C. Shoemaker R. G. Palmer 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1989,77(6):786-792
Summary Fifty-eight soybean accessions from the genus Glycine, subgenus Soja, were surveyed with 17 restriction fragment length polymorphism (RFLP) genetic markers to assess the level of molecular diversity and to evaluate the usefulness of previously identified RFLP markers. In general, only low levels of molecular diversity were observed: 2 of the 17 markers exhibited three alleles per locus, whereas all others had only two alleles. Thirty-five percent of the markers had rare alleles present in only 1 or 2 of the 58 accessions. Molecular diversity was least among cultivated soybeans and greatest between accessions of different soybean species such as Glycine max (L.) Merr. and G. soja Sieb. and Zucc. Principal component analysis was useful in reducing the multidimensional genotype data set and identifying genetic relationships. 相似文献
19.
细叶云南松天然种源林遗传多样性的SSR分析 总被引:2,自引:0,他引:2
利用12对SSR引物对三个不同种源的细叶云南松群体遗传多样性进行研究。结果表明:共检测到13个位点37个等位基因,每个位点平均观察等位基因数(A)为2.85,多态率为100%;平均有效等位基因数(Ne)1.45。各群体内的有效等位基因数平均为1.447,观察杂合度平均为0.341,期望杂合度平均为0.281。三个群体的Nei’s基因多样度指标的变化范围为0.256~0.297,Shannon多样性指数变化范围为0.448~0.484,各群体间的多态性水平差异不大。细叶云南松群体间的基因分化系数(Gst)为0.089,群体间的遗传分化水平较低,大部分变异均存在群体内。细叶云南松群体间的基因流(Nm)在不同位点的变化范围从4.693~122.189,平均为11.17。说明细叶云南松群体间存在比较充分的基因交流。 相似文献
20.
Douglas E. Soltis Pamela S. Soltis 《Evolution; international journal of organic evolution》1989,43(3):586-594
Although there is an extensive literature on the genetic attributes of allopolyploids, very little information is available regarding the genetic consequences of autopolyploidy in natural populations. We therefore addressed the major predicted genetic consequences of autopolyploidy using diploid and tetraploid populations of Tolmiea menziesii. Individual autotetraploid plants frequently maintain three or four alleles at single loci: 39% of the 678 tetraploid plants exhibited three or four alleles for at least one locus. Heterozygosity was also significantly higher in autotetraploid populations than in diploid populations: H° = 0.070 and 0.237 in diploid and tetraploid Tolmiea, respectively. Most of the genetic diversity in T. menziesii is maintained within populations (ratio of gene diversity within populations to mean total genetic diversity = 0.636). The total genetic diversity due to differentiation between the two cytotypes is only 0.055. Such a low degree of differentiation between cytotypes would be expected between a diploid and its autotetraploid derivative. Most diploid and all tetraploid populations examined are in genetic equilibrium. Diploid and tetraploid Tolmiea share three or four alleles at six of eight polymorphic loci. This suggests that either autotetraploid Tolmiea was formed via crossing of genetically different diploids (perhaps via a triploid intermediate) or autopolyploidy occurred more than once in separate individual plants, followed by later crossing of autotetraploids. 相似文献