Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA.

ABSTRACT: The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.

SUBMITTER: Wang D

PROVIDER: S-EPMC6972953 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Seasonal variations in food resource partitioning among four sympatric gudgeon species in the upper Yangtze River.

Project description:Knowledge of food resource partitioning among sympatric fish species is crucial for understanding the potential mechanisms of species coexistence. Gudgeons (Teleostei: Cyprinidae: Gobioninae) often dominate fish assemblages in the upper Yangtze River. However, little research has been conducted on their trophic interactions. In this paper, seasonal diet and feeding strategy variations of four sympatric gudgeon species, Coreius guichenoti, Coreius heterodon, Rhinogobio ventralis, and Rhinogobio cylindricus, were investigated by analysis of intestinal tract contents, aiming to explore whether food resource partitioning occurred among them. Fish specimens were collected during spring (April-May) and autumn (August-October) in 2010 in Hejiang, a free-flowing stretch of the upper Yangtze River. Coreius guichenoti, C. heterodon, and R. cylindricus showed omnivorous feeding habits, while R. ventralis exhibited an obligate carnivore feeding habit. Diet overlap among the four studied species was high, especially in spring. However, changes in feeding strategies were observed in autumn. Specifically, C. guichenoti and R. cylindricus expanded their dietary niche breadth and consumed detritus, Sinopotamidae or Hydropsychidae as important complementary food resources. In contrast, C. heterodon and R. ventralis reduced their dietary niche breadth and became more specialized on mussels (Limnoperna lacustris). These results confirmed that sympatric fish species can coexist with high diet overlap, and food resource partitioning among these species may also fluctuate with the seasons.

| S-EPMC6662251 | biostudies-literature

Genetic structure of two sympatric gudgeon fishes (Xenophysogobio boulengeri and X. nudicorpa) in the upper reaches of Yangtze River Basin.

Project description:BackgroundXenophysogobio boulengeri and X. nudicorpa are the only two species within the genus Xenophysogobio (Cyprinidae, Cypriniformes), and both are endemic to the upper reaches of the Yangtze River. In recent years, due to human activities, the natural resources available to both species have declined sharply. Sympatric species with overlapping niches inevitably compete for their habitats, and genetic structure and diversity can reflect population history and their potential for adaptation to changing environments, which is useful for management decisions.MethodsIn the present study, microsatellite DNA and mitochondrial DNA (mtDNA) markers were used to investigate the patterns of population genetic structure for X. boulengeri and X. nudicorpa. Microsatellite DNA data, jointly with traditional summary statistics including F ST and F is, were used to assess the population genetic structure by structure analysis. The mtDNA sequences were then used to examine these patterns through time to detect demographic history.ResultsXenophysogobio boulengeri and X. nudicorpa exhibited high levels of genetic diversity in Yangtze River populations, except for two populations of X. nudicorpa in the Jinsha River, which were low in mtDNA diversity. X. boulengeri showed genetic homogeneity among populations, whereas X. nudicorpa appeared to have significant geographic genetic divergence. Both species experienced a late-Pleistocene sudden population expansion in Yangtze River populations, but not in the Jinsha River populations of X. nudicorpa.DiscussionThe genetic homogeneity of X. boulengeri populations might result from similar population expansion events and environment features. The geographic genetic subdivision for X. nudicorpa between the Jinsha and Yangtze Rivers might be caused by the geographic isolation in the middle Pliocene, as well as climate and environmental heterogeneity.

| S-EPMC6688597 | biostudies-literature

Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights.

Project description:The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.

| S-EPMC6979408 | biostudies-literature

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River.

Project description:Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F-DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.

| S-EPMC6854117 | biostudies-literature

A new species of the gudgeon genus Huigobio Fang, 1938 (Cypriniformes: Cyprinidae) from the Yangtze River Basin, southern China.

Project description: Not available

| S-EPMC8743257 | biostudies-literature

Freshwater lake ecosystem shift caused by social-economic transitions in Yangtze River Basin over the past century.

Project description:Global lake systems have undergone rapid degradation over the past century. Scientists and managers are struggling to manage the highly degraded lake systems to cope with escalating anthropogenic pressures. Improved knowledge of how lakes and social systems co-evolved up to the present is vital for understanding, modeling, and anticipating the current and future ecological status of lakes. Here, by integrating paleoenvironmental, instrumental and historical documentary resources at multi-decadal scales, we demonstrate how a typical shallow lake system evolved over the last century in the Yangtze River Basin, an urbanized region containing thousands of shallow lakes. We find abrupt ecological shift happened in the lake ecosystem around the 1970s, with the significant reorganization of macrophyte, diatom and cladocera communities. The lake social-ecological system went through three stages as the local society transformed from a traditional agricultural before 1950s to an urbanized and industrialized society during the recent thirty years. The timing and interaction between social, economic and ecological feedbacks govern the transient and long-term dynamics of the freshwater ecosystem. Our results highlight the importance of accounting for the long-term dynamics and feedbacks between ecological, social and economic changes when defining safe operating spaces for sustainable freshwater ecosystem management.

| S-EPMC6249226 | biostudies-other

Adaptive gene expression divergence inferred from population genomics.

Project description:Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence. Genome-wide analyses, however, have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expression evolution. Here, we combined genomic expression data--analyzed in a phylogenetic context--with whole genome light-shotgun sequence data from six Drosophila simulans lines and reference sequences from D. melanogaster and D. yakuba. These data allowed us to use molecular population genetics to test for neutral versus adaptive gene expression divergence on a genomic scale. We identified recent and recurrent adaptive evolution along the D. simulans lineage by contrasting sequence polymorphism within D. simulans to divergence from D. melanogaster and D. yakuba. Genes that evolved higher levels of expression in D. simulans have experienced adaptive evolution of the associated 3' flanking and amino acid sequence. Concomitantly, these genes are also decelerating in their rates of protein evolution, which is in agreement with the finding that highly expressed genes evolve slowly. Interestingly, adaptive evolution in 5' cis-regulatory regions did not correspond strongly with expression evolution. Our results provide a genomic view of the intimate link between selection acting on a phenotype and associated genic evolution.

| S-EPMC2042001 | biostudies-literature

Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study.

Project description:Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.

| S-EPMC5103815 | biostudies-literature

The status of amur beak gudgeon Microphysogobio amurensis (Taranetz 1937) inferred from complete mitochondrial genome analysis.

Project description:The complete mitogenome sequence of Microphysogobio amurensis has been amplified and sequenced in this study. The overall base composition of M. amurensis mitogenome is: A (30%), C (26.8%), G (17.2%), T (26%), with an obvious A + T bias (56%). The assembled mitogenome, consisting of 16605 bp, has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. To estimate the status of M. amurensis, all available mitogenomes of Microphysogobio were downloaded from GenBank for phylogenetic analysis. The result strongly supported the traditional taxonomic hypothesis that M. amurensis was sister to M. brevirostris and M. koreensis. However, taxonomic confusion on its generic assignment remains to be further studied, as this study and other relevant molecular studies not only suggested that Microphysogobio could be divided in two major clusters (viz. the Palearctic species group and the Oriental species group), but also that two allied genera (Biwia, Rostrogobio) were embedded within the Palearctic species group of Microphysogobio.

| S-EPMC7800102 | biostudies-literature

Dataset on the distribution location and biological traits of freshwater fishes in the Yangtze River Basin.

Project description:In this data article, we provide the scientific and theoretical data on fish taxonomy including class, order, family, and genus in the Yangtze River. The Yangtze basin is divided into 56 units, and their geological information including latitude, longitude, latitude, and channel length is recorded. Fish presence/absence data at the unit scale are reported. Biological traits including morphological, physiological, and ecological characters of each fish species are also described, numeralized, and reported. These data are the foundation of the analyses and results in the article "Continental-scale analysis of taxonomic and functional fish diversity in the Yangtze River" (Kang et al., 2018).

| S-EPMC6226585 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data