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1.
Gobiobotia filifer is a small benthic fish distributed in Yangtze River Basin. The abundance of G. filifer increased after impoundment of Xiluodu Dam and Xiangjiaba Dam. The state of population structure and changes of genetic diversity before and after impoundment of Xiluodu Dam and Xiangjiaba Dam were interesting issues. However, efficient molecular markers were rare, which will limit us to solve above problems. Twenty‐eight expressed sequence tag SSRs (EST‐SSRs) were successfully identified and verified as stable amplification and polymorphic loci by polyacrylamide gel electrophoresis (PAGE) and capillary electrophoresis. The number of alleles at these EST‐SSR loci ranged from 3 to 14, the polymorphism information content values were 0.125–0.897, and the observed and expected heterozygosities were 0.0–0.857 and 0.132–0.928, respectively. Cross‐species amplification of the 28 loci developed in this study was examined in seven individuals of each of the 7 taxa. The amplification efficiency of 28 EST‐SSRs primer pairs is related to the distance of genetic relationship between cross‐species with G. filifer, and same subfamily species (Xenophysogobio boulengeri and Xenophysogobio nudicorpa) showed the highest (50%) amplification efficiency. These EST‐SSR markers could be used to analyse genetic diversity and population structure of G. filifer and related species.  相似文献   

2.
Mitochondrial 16S rDNA and CO I gene were used as molecular markers for the analysis of the genetic diversity and differentiation of Daphnia galeata populations in nine water bodies in the middle and lower reaches of the Yangtze River. In the combined 16S rDNA and CO I gene sequences, 54 variable sites and 44 haplotypes were observed among 219 individuals belonging to nine D. galeata populations. Average haplotype diversity and nucleotide diversity were, respectively, 0.72% and 0.56%. The F‐statistics (FST) value of the D. galeata populations was 0.149. According to the results of the neutral test, D. galeata in the middle and lower reaches of the Yangtze River had experienced a bottleneck effect in the history. Molecular variance analysis indicated that the genetic differentiation of the D. galeata populations mainly occurred within populations (85.09%). Greater genetic differentiations of D. galeata among individuals within populations appeared in the populations from the Huaihe River basin, whereas smaller genetic differentiations occurred in the populations from the middle reaches of the Yangtze River. Strong gene flows were all observed between Group I (four populations from the middle reaches of the Yangtze River) and Group ΙΙ (three populations from the middle and lower reaches of the Yangtze River), and Group ΙΙΙ (two populations from the Huaihe River basin). The effective migration rates (M) were 851.49 from Group I to Group ΙΙ and 685.96 from Group I to Group ΙΙΙ, respectively. However, no significant relationship was observed between the genetic differentiation and geographical distance of the nine populations (r = .137, p > .05). Results suggested that the genetic differentiation of D. galeata in the water bodies in the middle and lower reaches of the Yangtze River resulted mainly from geographical isolation.  相似文献   

3.
Geographical patterns, climate, and environmental change have important influences on the distribution and spread of aquatic organisms. However, the relationships between the geographical pattern and phylogenetics of Daphnia as well as environmental change are not well known. The genetic diversity and phylogeography of seven D. similoides sinensis populations located in the middle and lower reaches of the Yangtze River were investigated based on the combination of mitochondrial (COI gene) and nuclear (14 microsatellite primers) markers. Based on the mitochondrial gene markers, D. similoides sinensis from the middle and lower reaches of the Yangtze River had one ancestral haplotype and two evolutionary clades. In addition, D. similoides sinensis population deviated from neutral evolution, showing signs of a bottleneck effect followed by population expansion. Based on the microsatellite markers, the seven D. similoides sinensis populations formed three main groups. The dendrogram (NJ/ME) showed that D. similoides sinensis based on the mitochondrial genes marker were obviously clustered two main clades, whereas there were three clades based on the microsatellite markers. Our results suggested that the habitat fragmentation due to the barrier of the dams and sluices promoted the genetic differentiation and phylogeography of D. similoides sinensis populations in the middle and lower reaches of the Yangtze River.  相似文献   

4.
5.
Little has been known about the impacts of past vicariance events on the phylogeography and population structure of freshwater fishes in East Asia. The aims of this study are to assess the genetic variability with extensive sampling throughout the range of Chinese spiny loach, Cobitis sinensis, and to infer the genetic structure and evolutionary history of populations. Cobitis sinensis in China may have initiated from two ancestral populations, namely Yangtze and Pearl Rivers, which diverged about 7.24 MYA likely due to drainage systems alteration. In the phylogroup I, a southward dispersal event occurred from East China (Yangtze River) to south ZheMin and Hainan subregions, followed by eastward dispersal from ZheMin to south Taiwan. In the phylogroup II, eastward colonization took place from Pearl River to north Taiwan in the late Pliocene, coupled with loss of genetic diversity in the island populations. This study showed that Cenozoic tectonic movements and climatic and sea‐level fluctuations may have shaped the genetic structure of C. sinensis in concert. Highly diverged mtDNA sequences suggest existence of cryptic species in morphospecies C. sinensis.  相似文献   

6.
Parrotia subaequalis (Hamamelidaceae) is a Tertiary relic species endemic in eastern China. We used inter‐simple sequence repeat (ISSR) markers to access genetic diversity and population genetic structure in natural five populations of P. subaequalis. The levels of genetic diversity were higher at species level (= 0.2031) but lower at population level (= 0.1096). The higher genetic diversity at species levels might be attributed to the accumulation of distinctive genotypes which adapted to the different habitats after Quaternary glaciations. Meanwhile, founder effects on the early stage, and subsequent bottleneck of population regeneration due to its biological characteristics, environmental features, and human activities, seemed to explain the low population levels of genetic diversity. The hierarchical AMOVA revealed high levels (42.60%) of among‐population genetic differentiation, which was in congruence with the high levels of Nei's genetic differentiation index (GST = 0.4629) and limited gene flow (Nm = 0.5801) among the studied populations. Mantel test showed a significant isolation‐by‐distance, indicating that geographic isolation has a significant effect on genetic structure in this species. Unweighted pair‐group method with arithmetic average clustering, PCoA, and Bayesian analyses uniformly recovered groups that matched the geographical distribution of this species. In particular, our results suggest that Yangtze River has served as a natural barrier to gene flow between populations occurred on both riversides. Concerning the management of P. subaequalis, the high genetic differentiation among populations indicates that preserving all five natural populations in situ and collecting enough individuals from these populations for ex situ conservation are necessary.  相似文献   

7.
Within the plant kingdom, many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridize. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing Geum urbanum, sister species that hybridize in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd‐RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2–3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster‐ and species‐specific marker analyses revealed that, apart from four early‐generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1–3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.  相似文献   

8.
Little is known about the natural history, biology, and population genetic structure of the Hardhead Silverside, Atherinomorus stipes, a small schooling fish found around islands throughout the Caribbean. Our field observations of A. stipes in the cays of Belize and the Florida Keys found that populations tend to be in close association with the shoreline in mangrove habitats. Due to this potential island‐based population structuring, A. stipes represents an ideal system to examine questions about gene flow and isolation by distance at different geographic scales. For this study, the mitochondrial gene nd2 was amplified from 394 individuals collected from seven different Belizean Cays (N = 175) and eight different Floridian Keys (N = 219). Results show surprisingly high haplotype diversity both within and between island‐groups, as well as a high prevalence of unique haplotypes within each island population. The results are consistent with models that require gene flow among populations as well as in situ evolution of rare haplotypes. There was no evidence for an isolation by distance model. The nd2 gene tree consists of two well‐supported monophyletic groups: a Belizean‐type clade and a Floridian‐type clade, indicating potential species‐level differentiation.  相似文献   

9.
Host shifts are a key mechanism of parasite evolution and responsible for the emergence of many economically important pathogens. Varroa destructor has been a major factor in global honeybee (Apis mellifera) declines since shifting hosts from the Asian honeybee (Apis cerana) > 50 years ago. Until recently, only two haplotypes of V. destructor (Korea and Japan) had successfully host shifted to A. mellifera. In 2008, the sister species V. jacobsoni was found for the first time parasitizing A. mellifera in Papua New Guinea (PNG). This recent host shift presents a serious threat to world apiculture but also provides the opportunity to examine host shifting in this system. We used 12 microsatellites to compare genetic variation of V. jacobsoni on A. mellifera in PNG with mites on A. cerana in both PNG and surrounding regions. We identified two distinct lineages of V. jacobsoni reproducing on A. mellifera in PNG. Our analysis indicated independent host shift events have occurred through small numbers of mites shifting from local A. cerana populations. Additional lineages were found in the neighbouring Papua and Solomon Islands that had partially host shifted to A. mellifera, that is producing immature offspring on drone brood only. These mites were likely in transition to full colonization of A. mellifera. Significant population structure between mites on the different hosts suggested host shifted V. jacobsoni populations may not still reproduce on A. cerana, although limited gene flow may exist. Our studies provide further insight into parasite host shift evolution and help characterize this new Varroa mite threat to A. mellifera worldwide.  相似文献   

10.
11.
The population structure of benthic marine organisms is of central relevance to the conservation and management of these often threatened species, as well as to the accurate understanding of their ecological and evolutionary dynamics. A growing body of evidence suggests that marine populations can be structured over short distances despite theoretically high dispersal potential. Yet the proposed mechanisms governing this structure vary, and existing empirical population genetic evidence is of insufficient taxonomic and geographic scope to allow for strong general inferences. Here, we describe the range‐wide population genetic structure of an ecologically important Caribbean octocoral, Gorgonia ventalina. Genetic differentiation was positively correlated with geographic distance and negatively correlated with oceanographically modelled dispersal probability throughout the range. Although we observed admixture across hundreds of kilometres, estimated dispersal was low, and populations were differentiated across distances <2 km. These results suggest that populations of G. ventalina may be evolutionarily coupled via gene flow but are largely demographically independent. Observed patterns of differentiation corroborate biogeographic breaks found in other taxa (e.g. an east/west divide near Puerto Rico), and also identify population divides not discussed in previous studies (e.g. the Yucatan Channel). High genotypic diversity and absence of clonemates indicate that sex is the primary reproductive mode for G. ventalina. A comparative analysis of the population structure of G. ventalina and its dinoflagellate symbiont, Symbiodinium, indicates that the dispersal of these symbiotic partners is not coupled, and symbiont transmission occurs horizontally.  相似文献   

12.
Gynostemma pentaphyllum, a member of family Cucurbitaceae, is a perennial creeping herb used as a traditional medicinal plant in China. In this study, six polymorphic nSSR and four EST‐SSR primers were used to genotype 1,020 individuals in 72 wild populations of G. pentaphyllum. The genetic diversity and population structure were investigated, and ecological niche modeling was performed to reveal the evolution and demographic history of its natural populations. The results show that G. pentaphyllum has a low level of genetic diversity and high level of variation among populations because of pervasive asexual propagation, genetic drift, and long‐term habitat isolation. Results of the Mantel test demonstrate that the genetic distance and geographic distance are significantly correlated among G. pentaphyllum natural populations. The populations can be divided into two clusters on the basis of genetic structure. Asymmetrical patterns of historical gene flow were observed among the clusters. For the contemporary, almost all the bidirectional gene flow of the related pairs was symmetrical with slight differences. Recent bottlenecks were experienced by 34.72% of the studied populations. The geographic range of G. pentaphyllum continues to expand northward and eastward from Hengduan Mountains. The present distribution of G. pentaphyllum is a consequence of its complex evolution. Polyploidy in G. pentaphyllum is inferred to be polygenetic. Finally, G. pentaphyllum is a species in need of protection, so in situ and ex situ measures should be considered in the future.  相似文献   

13.
The genus Ditylenchus contains more than 80 recognized nematode species with a very wide host range. The most serious species are Ditylenchus dipsaci and Ditylenchus destructor. Populations of D. dipsaci species complex were collected from Allium cepa, Cichorium endivia and Phlox paniculata in Poland. The Ditylenchus gigas population was collected from Vicia faba minor, and populations of D. destructor, from Solanum tuberosum spp. tuberosum. Analyses of the rDNA sequences spanning both ITS1 and ITS2 fragment regions were carried out on the collected populations. The obtained DNA sequences were compared with those DNA sequences deposited in GenBank of populations isolated in other countries. Phylogenetic analysis was performed using the data obtained from the DNA sequence comparisons. The results indicated that there is no clear distinction between European and non‐European populations within D. dipsaci. The results also showed no clear distinction between populations isolated from different host plant species, including populations found in Poland. The populations of D. destructor described here constitute a common group together with American and Chinese populations belonging to the haplotype C of the D. destructor species. On the other hand, the D. gigas population was localized separately from those populations that have been described up until now, from Europe and Africa. This is also the first report on the occurrence of D. gigas in Poland.  相似文献   

14.
Sequence polymorphism at the MHC class II DRB locus was investigated in three finless porpoise (Neophocaena phocaenoides) populations in Chinese waters. Intragenic recombination and strong positive selection were the main forces in generating sequence diversity in the DRB gene. MHC sequence diversity changed significantly along the study period. Significant decrease in heterozygosity and lost alleles have been detected in the Yangtze River population and South China Sea population since 1990. Furthermore, there is a trend of increasing population differentiation over time. Especially, the genetic differentiation between the Yangtze River population and the Yellow Sea population was very low prior to 1990 (F ST = 0.036, P = 0.009), but became very significant after 1990 (F ST = 0.134, P < 0.001), suggesting a recent augmentation of genetic differentiation between both populations probably in a relatively short-term period. Porpoises from the Yangtze River displayed divergent frequencies of shared and private alleles from those displayed by two marine populations, which suggest that the former riverine population has been under a different selection regime (characteristic of a fresh water environment) than that of its marine counterparts.  相似文献   

15.
Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re‐entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region‐specific lineages. Here, we integrate several end points derived from high‐throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping‐by‐sequencing and whole‐genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from diverse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field‐caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.  相似文献   

16.
Morphologically similar populations of Aphanius that are currently considered as A. sophiae inhabit the endorheic Kor River Basin in the Zagros Mountains. Using genetic analysis based on mtDNA (cytochrome b), combined with examination of morphology (morphometry, meristics, otoliths), we discovered that what is thought to be A. sophiae is actually two distinct species, one of which is described as A. shirini sp. n. The males of the new species can be distinguished from those of all other Iranian inland Aphanius species by having only 7–10 clearly defined white flank bars, which is the lowest number of flank bars among the Iranian inland Aphanius species. Both males and females differ from all other Iranian inland Aphanius species by having a significantly longer caudal peduncle and a smaller dorsal fin depth. Based on the PhyML and Bayesian likelihood trees, A. shirini is sister to A. vladykovi from the Karoun Basin in the Zagros Mountains. Our results indicate that an ancient exorheic Kor River Basin existed in the Late Miocene and Pliocene. The close phylogenetic relationship between A. shirini and A. vladykovi suggests that the pre‐Pliocene drainage in the ancient Kor River Basin was directed to the north‐west (to the Karoun Basin), and not to the south‐east as in the present‐day Kor Basin. Both A. shirini and A. vladykovi represent the highest altitude records for Aphanius. We conclude that the splits of A. shirini and A. vladykovi can be linked to tectonic events in the Middle to Late Miocene, which created the highest altitudes (>3000 m) in the Zagros Mountains, and led to isolation of populations. The present‐day endorheic Kor Basin is known to have formed in the Late Pleistocene or Early Holocene, and the ‘young’ age of A. sophiae is clearly related to this history. Our results contribute to elucidate the link between geological history and the present‐day species diversity in the tectonically still active Zagros Mountains of Iran.  相似文献   

17.

Aim

To date, few studies have examined the phylogenetics of Corbicula clams in their native range and the environmental parameters influencing their distribution, although this could provide great insights into the biological adaptation and invasion dynamics of Corbicula clams. We sought to identify the genetic lineages of native Corbicula clams and elucidate the environmental factors shaping the distributions of identified lineages.

Location

China, mainly the Yangtze River Basin.

Methods

The alignment comprised 558 COI sequences including samples from China and 222 COI sequences from published studies. This dataset was used to generate phylogenetic trees and compare population diversity. We used dbRDA method to assess the relationship between these COI data and environmental factors measured to identify the important factors affecting Corbicula's distribution.

Results

The COI phylogenetic tree delineated the monophyly of 3 major COI clades and 77 distinct COI haplotypes in the Yangtze River Basin. The invasive lineage C/S (FW17) was not identified in our sampling in China, while invasive lineages A/R (FW5 = Hap6), B (FW1 = Hap17) and Rlc (FW4 = Hap43) were identified, abundant and widely distributed in the middle and lower reaches of Yangtze River. Focusing on populations from Yangtze River Basin, both the COI haplotype and nucleotide diversity in the lakes along the Yangtze River increased with longitude, except for the river mouth population. The AMOVA tests showed significant differentiation between the middle and lower reaches of the Yangtze River and among populations. The dbRDA results suggested that the parameter chloride explained most of the spatial COI haplotype distribution variation in the Yangtze River Basin, with the three invasive lineages tolerating broad fluctuations of salinity (chloride levels ranging from 4 to 60 mg/L).

Conclusions

The Corbicula COI haplotypes found within the Yangtze River Basin had distinct distribution preferences, with the invasive androgenetic lineages being the most abundant and widely distributed. Genetic diversity was higher in this native region than in invaded areas in Europe and America, while it decreased with increasing distance from the river mouth. Salinity appeared to be the main environmental factor shaping the COI haplotype distribution of Corbicula lineages within their native range.  相似文献   

18.
The snail Melanoides tuberculata has been used successfully in the control of some snails, intermediate host of parasitosis. Melanoides tuberculata has been found in Tunisia, but its effects on populations of native snail have not yet been evaluated in the field. Our objective is to determine whether M. tuberculata competed with Galba truncatula, using a field study. Twelve monthly investigations were carried out along an irrigation system in Ain Soltane's oasis (southwest of Tunisia). Here, we describe the population dynamics of G. truncatula with and without M. tuberculata in two stations: a witness pilot station (S1), in which the snail lives alone, and an experimental station (S2), where two species live together. The abundance of G. truncatula varied according to subsistence or not of M. tuberculata. The number of annual generations is higher in S1 (four generations) than S2 (two generations). In the absence of other molluscs or predators that can influence the density of G. truncatula and assuming that climatic factors are mitigated by the presence of an oasean microclimate, these results show that the mollusc M. tuberculata has a competition with the vector species of fluke.  相似文献   

19.
Miscanthus lutarioriparius is an endemic species that grows along the middle and lower reaches of the Yangtze River and is a valuable source of germplasm for the development of second‐generation energy crops. The plant that propagates via seeds, stem nodes, and rhizomes shows high phenotypic variation and strong local adaptation. Here, we examined the magnitude and spatial distribution of genetic variation in M. lutarioriparius across its entire distributional range and tested underlying factors that shaped its genetic variation. Population genetic analyses were conducted on 644 individuals from 25 populations using 16 microsatellite markers. M. lutarioriparius exhibited a high level of genetic variation (HE = 0.682–0.786; A= 4.74–8.06) and a low differentiation (FST = 0.063; Dest = 0.153). Of the total genetic variation, 10% was attributed to the differences among populations (df = 24, < 0.0001), whereas 90% was attributed to the differences among individuals (df = 619, ≤ 0.0001). Genetic diversity did not differ significantly across longitudes and did not increase in the populations growing downstream of the Yangtze River. However, significant associations were found between genetic differentiation and spatial distance. Six genetic discontinuities were identified, which mostly distributed among downstream populations. We conclude that anthropogenic factors and landscape features both contributed to shaping the pattern of gene flow in M. lutarioriparius, including long‐distance bidirectional dispersal. Our results explain the genetic basis of the high degree of adaptability in M. lutarioriparius and identify potential sources of new germplasm for the domestication of this potential second‐generation energy crop.  相似文献   

20.
Recently, molecular analyses revealed that African and Eurasian golden jackals are distinct species. This finding suggests re‐investigation of the phylogenetic relationships and taxonomy of other African members of the Canidae. Here, we provide a study on the phylogenetic relationship between populations of African jackals Lupulella mesomelas and L. adusta inferred from 962 bp of the mitochondrial cytochrome b (cytb) gene. As expected from its disjunct distribution, with one population in eastern Africa and the other one in southern Africa, we found two mitochondrial lineages within L. mesomelas, which diverged about 2.5 million years ago (Ma). In contrast, in L. adusta with its more continuous distribution in sub‐Saharan Africa, we found only a shallower genetic diversification, with the exception of the West African population, which diverged around 1.4 Ma from the Central and East African populations. Both divergence ages are older than, for example the 1.1–0.9 million years between the grey wolf Canis lupus and the African golden wolf C. lupaster. One taxonomic implication of our findings might be that the two L. mesomelas populations warrant species status. However, genome‐wide data with adequate geographical sampling are needed to substantiate our results.  相似文献   

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