Find research datasets worth reusing

opencc-zeroDec 2018View details →

Data from: A complex pattern of post-divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

The well-known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments and 5 nuclear loci of Dipelta floribunda and D. yunnanensis, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best-fit model supported by the approximate Bayesian computation (ABC) analysis indicated that, D. floribunda and D. yunnanensis diverged during the mid-Pleistocene period, consistent with the largest glacial period in the Qinghai-Tibet Plateau (QTP). The historically inter-specific gene flow was identified but seemed to have ceased after the last interglacial period (LIG), when the range of D. floribunda moved northward from the south of the Sichuan Basin. Further, populations of D. floribunda had expanded obviously in the north of the Sichuan Basin after the last glacial maximum (LGM). Relatively, the range of D. yunnanensis expanded before the LGM, reduced during the post-LGM especially in the north of the Sichuan Basin, reflecting the asynchronous responses of related species to the contemporary climate changes. Our results suggested that complex topography should be considered in understanding the distributional patterns even for closely related species and their demographic responses.

opencc-zeroDec 2018View details →

Data from: Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression.

Aim: We used genome-scale sampling to assess the phylogeography of a group of topminnows in the Fundulus notatus species complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assess the timing and pattern of range expansion in the context of late-Pleistocene-Holocene drainage events, and evaluate the evidence for introgressive hybridization between species. Location: Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands. Taxon: Topminnows, Genus Fundulus, subgenus Zygonectes - Fundulus notatus, Fundulus olivaceus, Fundulus euryzonus Methods: We sampled members of the F. notatus species complex throughout their respective ranges, including numerous drainage systems where species co-occur. We collected genome-wide Single Nucleotide Polymorphisms (SNPs) using the Genotype by Sequencing (GBS) method, and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed included STRUCTURE, Principle Coordinates Analysis, TreeMix and Approximate Bayesian Computation. Results: Genetic data are presented for 749 individuals sampled from 14 F. notatus, 20 F. olivaceus, and two F. euryzonus populations. Members of the species complex differed in phylogeographic structure, with F. notatus exhibiting geographic clusters corresponding to Pleistocene coastal drainages, and F. olivaceus comparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage. Main Conclusions: Populations of F. notatus and F. olivaceus exhibited contrasting patterns of lineage diversity among coastal drainages, indicating inter-specific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co-occur, in a pattern that is correlated with previous estimates of hybridization rates.

opencc-zeroSep 2021View details →

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239. The land snail Ellobium chinense (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense based on COI and 10 microsatellite markers. The analyses of 140 COI data from South Korea and Japan and 54 microsatellite data from South Korea revealed that E. chinense has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined E. chinense populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

publicJun 2019View details →

Data from: A complex pattern of post-divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Open the record for dataset details and reuse information.

publicSep 2021View details →

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation

Open the record for dataset details and reuse information.

publicJun 2019View details →

Data from: Late Pleistocene range expansion of North American topminnows accompanied by admixture and introgression.

Open the record for dataset details and reuse information.

opencc-zeroDec 2009View details →

Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow

Range expansions and gene flow as micro-evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic populations in order to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples and thus restricted to a single population. Analysis of molecular variance revealed that most of the variation was within populations with no significant genetic structuring on either side of the Atlantic. Demographic analyses indicated that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced a slight trend of increase in population size over time, whereas EC (the English Channel) area experienced expansion beginning approximately 170,000-360,000 BP. The observed complex genetic pattern of C. crispus is consistent with a scenario of multiple unrelated founding events by survival of this species in at least three putative Pleistocene refugia along the European coastline, and subsequent trans-Atlantic dispersal combined with contiguous northward population expansion predating the LGM and geographically gene flow.

opencc-zeroDec 2017View details →

Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia

Phylogeographic patterns of trees in topographically subdued, unglaciated landscapes are under-reported, and might reflect population persistence and the influences of environment and distance over historical (~2.6Mya-present) and contemporary (recent generations) time-scales. We examined this hypothesis using genetic analyses of four slowly evolving non-coding chloroplast sequences and 16 nuclear microsatellites in the tree Corymbia calophylla from south-western Australia that has been unglaciated since the Permian (.300-250Mya). We found strong population differentiation for chloroplast DNA and low differentiation for nuclear loci, consistent with higher gene flow by pollen than seed. We identified three divergent chloroplast lineages distributed in central, north and south geographic regions, and diversifying from the early (.3.028Mya), mid- (.0.793Mya) and late- (.0.426Mya) Pleistocene, respectively. Moderate-high nucleotide diversity with population-specific haplotypes supported long-term persistence but diversification of lineages provided evidence of unexpected episodic range expansion. We suggest this pattern reflects environmental influences of climatic oscillations during progressive drying of south-western Australia from the early Pleistocene. Significant tests for isolation by environment for nuclear loci also supported an influence of contemporary environmental (aridity) conditions on genetic structure, but isolation by distance (IBD) was greater. Significant chloroplast and nuclear IBD suggested distance was a major influence on gene flow at both time-scales.

opencc-zeroDec 2014View details →

Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1–0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.

opencc-zeroDec 2012View details →

Data from: Pliocene intraspecific divergence and Plio-Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai-Tibet Plateau

A knowledge of intraspecific divergence and range dynamics of dominant forest trees in response to past geological and climate change is of major importance to an understanding of their recent evolution and demography. Such knowledge is informative of how forests were affected by environmental factors in the past and may provide pointers to their response to future environmental change. However, genetic signatures of such historical events are often weak at individual loci due to large effective population sizes and long generation times of forest trees. This problem can be overcome by analysing genetic variation across multiple loci. We used this approach to examine intraspecific divergence and past range dynamics in the conifer Picea likiangensis, a dominant tree of forests occurring in eastern and southern areas of the Qinghai-Tibet Plateau (QTP). We sequenced 13 nuclear loci, two mitochondrial DNA regions and three plastid (chloroplast) DNA regions in 177 individuals sampled from 22 natural populations of this species, and tested the hypothesis that its evolutionary history was markedly affected by Pliocene QTP uplifts and Quaternary climatic oscillations. Consistent with the taxonomic delimitation of the three morphologically divergent varieties examined, all individuals clustered into three genetic groups with inter-variety admixture detected in regions of geographical overlap. Divergence between varieties was estimated to have occurred within the Pliocene and ecological niche modeling based on 20 ecological variables suggested that niche differentiation was high. Furthermore, modeling of population genetic data indicated that two of the varieties (var. rubescens and var. linzhiensis) expanded their population sizes after the largest Quaternary glaciation in the QTP, while expansion of the third variety (var. likiangensis) began prior to this, probably following the Pliocene QTP uplift. These findings point to the importance of geological and climatic changes during the Pliocene and Pleistocene as causes of intraspecific diversification and range shifts of dominant tree species in the QTP biodiversity hotspot region.

opencc-zeroFeb 2022View details →

Pleistocene range expansion throughout the Mediterranean and back-colonization from the Canary Islands in the legume Bituminaria bituminosa

Aim: Species with widespread distributions offer excellent opportunities for investigating recent biogeographical patterns across broad scales. Here, we tested the hypothesis that, due to its intermediate geographical location, NW Africa is pivotal in explaining the phylogeographical patterns of taxa with Mediterranean-Macaronesian distributions using a legume species with short generation times. Region: Mediterranean, with a focus on NW Africa and the Canary Islands Taxon: Pitch trefoil ( Bituminaria bituminosa) Methods: We generated genetic data and performed phylogeographical and demographic analyses at two geographical scales: Mediterranean Basin (MB), using plastid sequences (115 individuals), and Macaronesia, using plastid sequences (182 individuals) and 10 nuclear microsatellite loci (220 individuals). We also performed a literature survey focusing on phylogeographical studies of other circum-Mediterranean taxa. Results: North-west Africa was identified as a center of genetic diversity (19 out of 38 haplotypes) and demographic expansion of B. bituminosa in the MB during the Pleistocene. Our literature review revealed two main phylogeographical patterns in widespread species: pre-Mediterranean evergreen sclerophylls vs. Pleistocene facultative-deciduous (including Bituminaria) taxa, but on average both functional groups show a similar, large genetic diversity (c. 40% of haplotypes) in NW Africa. At the Macaronesian scale, we found that Canarian Bituminaria is composed of two genetic sublineages that coexist and hybridize on the central islands and in the mainland Macaronesian enclave (Anti-Atlas region). Demographic analyses rejected the progression rule as the model of island colonization, but strongly suggested that Anti-Atlas populations are the result of back-colonization from the easternmost islands before the Last Glacial Maximum (LGM). Conclusions: Bituminaria displays a pattern of Quaternary eastward expansion in the MB that appears to be paralleled by several members of its functional plant group. Thus, our study reveals a previously undescribed dual role of NW Africa in plant biogeography, acting both as a source of species expansion to the rest of the MB and a LGM refugium of plant populations with a Macaronesian island origin.

Fig. 5 Landscape interpolations for the Plateau a and Piedmont b in Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus)

Fig. 5 Landscape interpolations for the Plateau a and Piedmont b clades based on genetic differentiation among COI haplotypes. Peaks (reddish colors) represent areas of high genetic diversity and valleys (blue colors) indicate areas of low diversity

Fig. 4 Species distribution models for Vaejovis carolinianus. Results were projected onto LGM conditions from MIROC a and CCSM4 b data sources invoking the model generated using current climates data c in Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus)

Fig. 4 Species distribution models for Vaejovis carolinianus. Results were projected onto LGM conditions from MIROC a and CCSM4 b data sources invoking the model generated using current climates data c. Localities used to test and train the model are indicated by

Fig. 1 in Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus)

Fig. 1 Map depicting the distribution of Vaejovis carolinianus samples in relation to major rivers in the southeastern United States. Circle color corresponds to mitochondrial haplotypes in Figs. 2 and 3. Circle size is proportional to sample size

Fig. 3 in Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus)

Fig. 3 Bayesian chronogram, haplotype networks, and Bayesian skyline plots generated with COI data from Vaejovis carolinianus. The chronogram was generated using a rate calibration in BEAST and depicts major V. carolinianus clades. Two large clades, Plateau and Piedmont, are collapsed for clarity. Numbers above nodes indicate posterior probabilities. Mean age estimates and 95% HPD estimates

Fig. 2 in Pliocene origins, Pleistocene refugia, and postglacial range expansions in southern devil scorpions (Vaejovidae: Vaejovis carolinianus)

Fig. 2 Mitochondrial (COI) phylogeny, nuclear (ITS-2) haplotype network, and PCA identifying clades within V. carolinianus. a Bayesian consensus phylogeny generated with COI data in MrBayes. Bayesian posterior probabilities and Maximum Likelihood bootstrap values are above nodes. b Median-joining haplotype network

publicMar 2015View details →

Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Open the record for dataset details and reuse information.

publicJan 2018View details →

Data from: Persistence with episodic range expansion from the early Pleistocene: the distribution of genetic variation in the forest tree Corymbia calophylla (Myrtaceae) in south-western Australia

Open the record for dataset details and reuse information.

publicJan 2014View details →

Data from: Evolutionary history of the Maltese wall lizard Podarcis filfolensis: insights on the ‘Expansion-Contraction’ model of Pleistocene biogeography

Open the record for dataset details and reuse information.