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1.
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Sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) are the most important timber species in Japan. To quantify and compare the level of nucleotide variation in these species, we investigated their variation at ten nuclear loci. Average values of nucleotide diversity at synonymous sites (π SYN) found in sugi and hinoki were 0.0038 and 0.0069, respectively. However, although the average value of nucleotide diversity was higher in hinoki than in sugi, their average values of haplotype diversity were similar. Deviations from the standard neutral model were detected at two loci in hinoki using Tajima’s D, Fay and Wu’s H, and Strobeck’s S statistics, which seem to be due to its historical population structure. Levels of divergence between the two species at synonymous sites of the ten genes ranged from 0.121 to 0.566 (0.28 on average). These values positively correlated with their guanine + cytosine contents at third-codon positions of synonymous sites (%GC3s).  相似文献   

3.
Japanese eels are widely distributed in northeast Asian countries, and they have a catadromous life history. In this article, we explored whether Japanese elvers have temporal genetic structure and whether the population went through population expansion during the Pleistocene. In total, 273 specimens were collected from the Tanshui River estuary, northern Taiwan, in 1989–2008. The highly variable region of the mitochondrial DNA D-loop was cloned and sequenced. A genealogy was reconstructed based on the Neighbor-joining method, and results showed an unobvious yearly clade and a high level of haplotype diversity, but low mean nucleotide diversity among samples. Most of the pairwise F ST appeared statistically insignificant. These genetic parameters suggested a lack of temporal population structure combined with a sustainable high effective population size of Japanese eels. Negative values of Tajima’s D and Fu’s F s appeared in all samples with high significance. The mismatch distribution, skyline plot, and minimum spanning network indicated that historical population expansion of the Japanese eel could be traced back to the Pleistocene. Results of this study imply the Japanese eel has a complex life history, and the temporal structure of Japanese eels should be continually monitored in the future.  相似文献   

4.
Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging, and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r 2 ≥ 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome wide LD at r 2 ≥ 0.2 was reduced to ~5–6 cM, providing evidence of the potential for association mapping of agronomically important traits in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations were confirmed in general linear model and structured association test, accounting for population structure and permutation-based multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments, were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at ‘moderate to strong’ and ‘strong to very strong’ evidence levels, suggesting their usefulness for marker-assisted breeding programs and overall effectiveness of association mapping using cotton germplasm resources. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

5.
Antigen B (AgB) is an excretory–secretory product of larval stage of Echinococcus granulosus. This antigen is abundantly secreted by larval stage of the worm. AgB is encoded by a multigene family and is suggested to be involved in evasion of host immune system. During the present study a total of 110 animal isolates of E. granulosus has been screened by mutation scan screening. A total of 14 conformers were detected on the basis of single strand banding profile of 129 bp fragment of AgB1 subunit. Analysis of sequence information of 14 conformers could cluster the isolates into two different group viz. buffalo–cattle and sheep–goat cluster. Conceptual amino acid sequence information of two clusters could be differentiated in terms of MHCII binding propensity of agretope and B-cell epitope region. This type of analysis of clustering of animal isolates on the basis of binding propensity towards different MHC antigens and B-cell linear epitope is the example of its own kind. Positive Tajima’s D value indicated that, AgB1 is under balancing selection pressure which might be considered as heterogeneous selection pressure exerted by the host.  相似文献   

6.
Various photoreceptors in plants are used to monitor important environmental light signals and regulate plant development. Despite their functional importance, recent studies have demonstrated that red/far-red absorbing phytochromes or blue/UV-A absorbing cryptochromes are involved in local adaptation within a species’ range. In the present study, to exemplify the intraspecific photoreceptor evolutionary pattern, the genetic structures of cryptochrome genes (CRY1 and CRY2) in Cardamine nipponica (Brassicaceae), of which PHYE, a gene coding one of the phytochromes, was found to be involved in local adaptation between central and northern Japanese populations. Although clear genetic differentiations between central and northern Japan were detected (CRY1: F ST = 0.63, CRY2: F ST = 0.53), overall nucleotide diversity was very low (CRY1: π Total = 0.0014, CRY2: π Total = 0.0013), and the polymorphism patterns were neutral (CRY1: Tajima’s D = 0.084, P = 0.32, CRY2: D = −0.014, P = 0.39). Therefore, the involvement of cryptochromes in the adaptation to local environments is difficult to postulate. Consequently, this study along with our previous findings suggest that intraspecific photoreceptor gene polymorphisms in C. nipponica were mostly suppressed by purifying selection due to their functional importance as photoreceptors, while some of the photoreceptors may play substantial roles in adaptation to local environments.  相似文献   

7.
Elongate loach (Leptobotia elongata (Bleeker)), an endemic fish species to China, is a famous ornamental freshwater fish. Here, a comparative study of mtDNA control region (D-loop) (835 bp) sequences was performed to analyze its wild population structure and evaluate the genetic diversity for 110 individuals from five locations in the upper reaches of the Yangtze River, China. A total of 49 polymorphic sites and 45 haplotypes yielded high haplotype diversity (h = 0.952), but low nucleotide diversity (π = 0.00454) as that of many fish species. Sequence divergences between haplotypes ranged from 0.0033 ± 0.0011 to 0.0050 ± 0.0012 in intra-groups, and from 0.0037 ± 0.0.0011 to 0.0050 ± 0.0012 between groups. Significant values of Tajima’s D (−1.86383, P < 0.01) and Fu’s F S (−25.93, P < 0.01), together with uni-modal mismatch distribution, indicated a recent genetic bottleneck or population expansion of the species. Analysis of molecular variance (AMOVA) indicated a small amount of differentiation among groups (1.7%); most of the total variation occurred within groups (98.3%). Also, there was no significant population structure (F ST = 0.017, P > 0.05), and estimates of gene flows among groups were extremely high (Nm = 28.88), suggesting low genetic divergence between populations in the species. The lack of genetic differentiation among groups is most likely due to the combined gene flow from the downstream movement of eggs and larvae with currents and the upstream or downstream migration of adults throughout the distribution. These groups of L. elongata distributed in upper reaches of the Yangtze River should be considered as a single management unit.  相似文献   

8.
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26–27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima’s D and Fu and Li’s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.  相似文献   

9.
One crucial feature of zygotic linkage disequilibrium (LD) analysis is its direct use of diploid genotyping data, irrespective of the type of mating system. Previous theories from an evolutionary perspective mainly focus on gametic LD, but the equivalent development for zygotic LD is not available. Here I study the evolution of zygotic LD and the covariances between gametic and zygotic LDs or between distinct zygotic LDs in a finite local population under constant immigration from a continent population. I derive the analytical theory under genetic hitchhiking effects or in a neutral process. Results indicate that zygotic LDs (diploid level) are more informative than gametic LD (haploid level) in indicating the effects of different evolutionary forces. Zygotic LDs may be greater than or comparable to gametic LD under the epistatic selection process, but smaller than gametic LD under the non epistatic selection process. The covariances between gametic and zygotic LDs are strongly affected by the mating system, linkage distance, and genetic drift effects, but weakly affected by seed and pollen flow and natural selection. The covariances between different zygotic LDs are generally robust to the effects of gene flow, selection, and linkage distance, but sensitive to the effects of genetic drift and mating system. Consistent patterns exist for the covariances between the zygotic LDs for the two-locus genotypes with one common genotype at one locus or without any common genotype at each locus. The results highlight that zygotic LDs can be applied to detecting natural population history.  相似文献   

10.
The objectives of this study were to explore cytogenetic variation and the role of chromosomal change on local adaptation and genetic differentiation of Chironomus circumdatus Kieffer from Thailand. A total of 1,505 larvae from 24 populations were examined cytologically. Twelve chromosomal inversions were found and most of these (9 of 12) were rare inversions. All populations were in Hardy–Weinberg equilibrium. Significant association (P < 0.001) between the A2 and B5 inversions was detected in one population. Population genetic structure analysis indicated significant genetic differentiation between populations (F ST = 0.037, P < 0.001). Geographic distance was the principal factor limiting gene flow between populations. Nei’s modified genetic distance (D A) between populations ranged from 0.001 to 0.011 with an average of 0.003. An UPGMA population phenogram depicting relationship between populations based on D A values revealed three groups of populations, group I, II and III each characterized by different inversions/inversion frequencies. Significant correlation of inversion C3 and water temperature suggested that this inversion might have a role to play on adaptation to high temperature habitat. However, if detection of significant population subdivision and relationship between genetic and geographic distance are taken into account, relationship between C3 and water temperature will also be due to the effect of migration/drift alone without the effect of selection.  相似文献   

11.
Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of nucleotide diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average πsil = 0.004) as compared to the SKn class (average πsil = 0.024). The multilocus nucleotide diversity at silent sites (θ W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r 2 of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.  相似文献   

12.
Monitoring the loss of genetic diversity in wild populations after a bottleneck event is a priority in conservation and management plans. Here, we used diverse molecular markers to search for signatures of demographic bottlenecks in two wolf populations; an isolated population from the Iberian Peninsula and a non-isolated population from European Russia. Autosomal, mtDNA and Y-chromosomal diversity and the effective population size (Ne) were significantly lower in the Iberian population. Neutrality tests using mtDNA sequences, such as R2, Fu and Li’s F*, Tajima’s D and Fu’s Fs, were positively significant in the Iberian population, suggesting a population decline, but were not significant for the Russian population, likely due to its larger effective population size. However, three tests using autosomal data confirmed the occurrence of the genetic bottleneck in both populations. The M-ratio test was the only one providing significant results for both populations. Given the lack of consistency among the different tests, we recommend using multiple approaches to investigate possible past bottlenecks. The small effective population size (about 50) in the Iberian Peninsula compared to the presumed extant population size could indicate that the bottleneck was more powerful than initially suspected or an overestimation of the current population. The risks associated with small effective population sizes suggest that the genetic change in this population should be closely monitored in the future. On the other hand, the relatively small effective population size for Russian wolves (a few hundred individuals) could indicate some fragmentation, contrary to what is commonly assumed.  相似文献   

13.
A founder event occurs when a new population is established from a small number of individuals drawn from a large ancestral population. Mayr proposed that genetic drift in an isolated founder population could alter the selective forces in an epistatic system, an observation supported by recent studies. Carson argued that a period of relaxed selection could occur when a founder population is in an open ecological niche, allowing rapid population growth after the founder event. Selectable genetic variation can actually increase during this founder-flush phase due to recombination, enhanced survival of advantageous mutations, and the conversion of non-additive genetic variance into additive variance in an epistatic system, another empirically confirmed prediction. Templeton combined the theories of Mayr and Carson with population genetic models to predict the conditions under which founder events can contribute to speciation, and these predictions are strongly confirmed by the empirical literature. Much of the criticism of founder speciation is based upon equating founder speciation to an adaptive peak shift opposed by selection. However, Mayr, Carson and Templeton all modeled a positive interaction of selection and drift, and Templeton showed that founder speciation is incompatible with peak-shift conditions. Although rare, founder speciation can have a disproportionate importance in adaptive innovation and radiation, and examples are given to show that "rare" does not mean "unimportant" in evolution. Founder speciation also interacts with other speciation mechanisms such that a speciation event is not a one-dimensional process due to either selection alone or drift alone.  相似文献   

14.
Castanea squinii Dode, an endemic tree widely distributed in China, plays an important role both in chestnut breeding and forest ecosystem function. The spatial genetic structure within and among populations is an important part of the evolutionary and ecological genetic dynamics of natural populations, and can provide insights into effective conservation of genetic resources. In the present study, the spatial genetic structure of a panmictic natural population of C. sequinii in the Dabie Mountain region was investigated using microsatellite markers. Nine prescreened microsatellite loci generated 29–33 alleles each, and were used for spatial autocorrelation analysis. Based on Moran’s I coefficient, a panmictic population of C. sequinii in the Dabie Mountain region was found to be lacking a spatial genetic structure. These results suggest that a high pollen-mediated gene flow among subpopulations counteract genetic drift and/or genetic differentiation and plays an important role in maintaining a random and panmictic population structure in C. sequinii populations. Further, a spatial genetic structure was detected in each subpopulation’s scale (0.228 km), with all three subpopulations showing significant fine-scale structure. The genetic variation was found to be nonrandomly distributed within 61 m in each subpopulation (Moran’s I positive values). Although Moran’s I values varied among the different subpopulations, Moran’s I in all the three subpopulations reached the expected values with an increase in distances, suggesting a generally patchy distribution in the subpopulations. The fine-scale structure seems to reflect restricted seed dispersal and microenvironment selection in C. sequinii. These results have important implications for understanding the evolutionary history and ecological process of the natural population of C. sequinii and provide baseline data for formulating a conservation strategy of Castanea species. __________ Translated from Acta Phytoecologica Sinica, 2006, 30(1): 147–156 [译自: 植物生态学报]  相似文献   

15.
The endangered Cook’s petrel (Pterodroma cookii) is restricted to two separated populations at the extremes of its former range across New Zealand. Prior work revealed morphological, foraging, and reproductive isolation between these two remnant populations. To aid the conservation management of the species, additional information is required on the genetic structure of Cook’s petrel. We used mitochondrial DNA sequences (Cytochrome Oxidase subunit 1 gene), collected from 26 and 19 Cook’s petrel breeding on Little Barrier Island (LBI) and Codfish Island (CDF), respectively, for this preliminary study. We uncovered distinct population genetic structure with analysis of molecular variance suggesting genetic isolation of the populations. Levels of genetic variation were higher in the LBI population (four haplotypes present; h = 0.34 and π = 0.10) whereas the CDF population had only one haplotype that was distinct from the LBI population. Our results indicate that Cook’s petrel constitute two distinct management units for which conservation of genetic as well as behavioural and morphological diversity should be a priority. Further genetic studies using nuclear markers are recommended.  相似文献   

16.
Previous theory indicates that zygotic linkage disequilibrium (LD) is more informative than gametic or composite digenic LD in revealing natural population history. Further, the difference between the composite digenic and maximum zygotic LDs can be used to detect epistatic selection for fitness. Here we corroborate the theory by investigating genome-wide zygotic LDs in HapMap phase III human populations. Results show that non-Africa populations have much more significant zygotic LDs than do Africa populations. Africa populations (ASW, LWK, MKK, and YRI) possess more significant zygotic LDs for the double-homozygotes (DAABB) than any other significant zygotic LDs (DAABb, DAaBB, and DAaBb), while non-Africa populations generally have more significant DAaBb’s than any other significant zygotic LDs (DAABB, DAABb, and DAaBB). Average r-squares for any significant zygotic LDs increase generally in an order of populations YRI, MKK, CEU, CHB, LWK, JPT, CHD, TSI, GIH, ASW, and MEX. Average r-squares are greater for DAABB and DAaBb than for DAaBB and DAABb in each population. YRI and MKK can be separated from LWK and ASW in terms of the pattern of average r-squares. All population divergences in zygotic LDs can be interpreted with the model of Out of Africa for modern human origins. We have also detected 19735-95921 SNP pairs exhibiting strong signals of epistatic selection in different populations. Gene-gene interactions for some epistatic SNP pairs are evident from empirical findings, but many more epistatic SNP pairs await evidence. Common epistatic SNP pairs rarely exist among all populations, but exist in distinct regions (Africa, Europe, and East Asia), which helps to understand geographical genomic medicine.  相似文献   

17.
Among rhesus macaques (Macaca mulatta)and other cercopithecine monkeys, social groups occupying adjacent home ranges (i.e., members of the same local population) exchange individuals and genes and thus exhibit marked genetic similarities. To assess the degree to which this pattern extends beyond the local population, the genetic structure of M. mulattaand six other primate species was determined using Nei’s (1973) gene-diversity analysis. The genetic similarities seen among social groups in the Dunga Gali population of M. mulatta (Melnick et al.,1984a) can be seen over the entire species range. Comparison of these results with the structures of other similarly organized primate species indicates that (1) the average social group contains most of its local population’s genetic diversity, (2) the average local population contains the majority of the genetic diversity found in the region to which it belongs, and (3) the proportion of species gene diversity found in the average regional population varies substantially between species. Genetic homogeneity within local and regional populations is probably the product of gene flow. The application of a number of analytical models of selection and gene flow strongly suggests that gene flow, genetic drift, and zoogeography offer a more parsimonious and plausible explanation for interspecific variation in regional differentiation than does stabilizing selection.  相似文献   

18.
This study determined the sequences of chloroplast DNA (cpDNA) trnL-F non-coding regions of individuals of a tropical coniferous species, Dacrydium pectinatum, collected from 12 natural populations located in Hainan Province, southern China. Sequence length varied from 868 bp to 876 bp, indicating length polymorphism. Base composition in the sequences was high in A+T content between 64.17% and 64.95%, and no recombination event occurred (Rm = 0). Thirty haplotypes were identified based on statistical parsimony algorithm by running the TCS program. Populations of D. pectinatum in Hainan were lacking genetic differentiation. Such a deduction was supported by the observed F ST values (0.00), AMOVA (24.17% of molecular variance attributed to difference among populations, P>0.05), high values of Nm (ranging from 1.92 to 2.50) and the branching structure in neighbor-joining (NJ) tree constructed from haplotypes. A ‘star-like’ pattern was exhibited in the TCS network of trnL-F haplotypes, and majority of the haplotypes coalesced near the tips in NJ tree. Gene genealogies of cpDNA haplotypes proposed a recent population expansion of D. pectinatum in Hainan, which was further supported by the results from Tajima’s D test and mismatch distribution analysis. Our data, in conjunction with geological and palynological evidences, showed that in the Holocene, due to global warming, refugee populations of D. pectinatum in Hainan might experience a range expansion. __________ Translated from Acta Scientiarum Naturalium Universitatis Sunyatseni, 2005, 44(5): 70–74 [译自: 中山大学学报 (自然科学版), 2005, 44(5): 70–74]  相似文献   

19.
Denmark lies on the edge of the distributional range of the brown hareLepus europaeus Pallas, 1778, where population differentiation is most likely to occur. A total of 369 brown hares from eight geographically distinct Danish European brown hare populations were used to study the genetic population structure. In all, 480bp of the mitochondrial D-loop were sequenced in both directions. Observed genetic diversity (π) was relatively low (π=0.41%) while haplotype diversity (h=0.808) and the number of unique haplotypes (19) were similar to levels found in other European brown hare populations. The observed population structure was pronounced (pairwise conventionalF ST and ϕ st ranged between 6.9–57% and 5–69.8%, respectively). There was no correlation between the geographic and the genetic distance. Population structure was influenced by genetic drift, anthropogenic effects (eg translocation and escapes from hare-farms) and by post-glacial recolonization from southern refuges or refuges north east of the Black Sea. Analysis of historical population expansion/fluctuation events indicated that the populations have experienced different demographic events in the recent past. Relatively high sequence divergence between some populations might be explained by multiple recolonization events after the last Pleistocene glaciations or by stocking effects. Colonization from southern refuges was supported by the observation that haplotype 2 in the Danish brown hare was identical to the central European ancestral haplotype c07.  相似文献   

20.
Biologists and philosophers have been extremely pessimistic about the possibility of demonstrating random drift in nature, particularly when it comes to distinguishing random drift from natural selection. However, examination of a historical case – Maxime Lamotte’s study of natural populations of the land snail, Cepaea nemoralis in the 1950s – shows that while some pessimism is warranted, it has been overstated. Indeed, by describing a unique signature for drift and showing that this signature obtained in the populations under study, Lamotte was able to make a good case for a significant role for␣drift. It may be difficult to disentangle the causes of drift and selection acting in a population, but it is not (always) impossible.  相似文献   

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