Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations

Inferring the history of isolation and gene flow during species divergence is a central question in evolutionary biology. The European river lamprey (Lampetra fluviatilis) and brook lamprey(L. planeri)show a low reproductive isolation but have highly distinct life histories, the former being parasitic-anadromous and the latter non-parasitic and freshwater resident. Here we used microsatellite data from six replicated population pairs to reconstruct their history of divergence using an approximate Bayesian computation framework combined with a random forest model. In most population pairs, scenarios of divergence with recent isolation were outcompeted by scenarios proposing ongoing gene flow, namely the Secondary Contact (SC) and Isolation with Migration (IM) models. The estimation of demographic parameters under the SC model indicated a time of secondary contact close to the time of speciation, explaining why SC and IM models could not be discriminated. In case of an ancient secondary contact, the historical signal of divergence is lost and neutral markers converge to the same equilibrium as under the less parameterized model allowing ongoing gene flow. Our results imply that models of secondary contacts should be systematically compared to models of divergence with gene flow; given the difficulty to discriminate among these models, we suggest that genome-wide data are needed to adequately reconstruct divergence history.

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Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

10.1101/2021.11.20.469217 ◽

2021 ◽

Author(s):

Zheng Li ◽

Jie Zhou ◽

Minzhi Gao ◽

Wei Liang ◽

Lu Dong

Keyword(s):

Sexual Selection ◽

Gene Flow ◽

Late Pleistocene ◽

Approximate Bayesian Computation ◽

De Novo ◽

Demographic History ◽

Population Expansion ◽

Secondary Contact ◽

Bayesian Computation ◽

Approximate Bayesian

Background: Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrid recordings in field. Methods: In this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) method based on the multiple genes data. With a new assembled de novo genome of Lady Amherst's pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC). Results: The results provide clear evidence that the gene flow between the two pheasants were consistent with the prediction of isolation with migration model for allopatric populations, indicating that there was long-term gene flow after the initially divergence (ca. 2.2 million years ago), and further support the secondary contact when included the parapatric populations since around 30 ka ongoing gene flow to now, which might be induced by the population expansion of the Golden pheasant in late Pleistocene. Conclusions: The results of the study support the scenario of speciation between Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae) with cycles of mixing-isolation-mixing due to the dynamics of natural selection and sexual selection in late Pleistocene that provide a good research system as evolutionary model to test reinforcement selection in speciation. Keywords: Golden pheasant (Chrysolophus pictus), Lady Amherst's pheasant (Chrysolophus amherstiae), speciation, gene flow, Approximate Bayesian Computation (ABC), Pairwise Sequentially Markovian coalescent (PSMC).

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Connection, isolation and reconnection: Quaternary climatic oscillations and the Andes shaped the phylogeographical patterns of the Patagonian bee Centris cineraria (Apidae)

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa116 ◽

2020 ◽

Vol 131 (2) ◽

pp. 396-416 ◽

Cited By ~ 1

Author(s):

María Sosa-Pivatto ◽

Gonzalo A Camps ◽

Matías C Baranzelli ◽

Anahí Espíndola ◽

Alicia N Sérsic ◽

...

Keyword(s):

Demographic History ◽

Joint Effect ◽

Secondary Contact ◽

Glacial Refugium ◽

Distribution Models ◽

Climatic Oscillations ◽

The Andes ◽

History Of ◽

Spatio Temporal ◽

Approximate Bayesian

Abstract The joint effect of the Andes as a geographical barrier and the Quaternary glaciations as promoters of genetic divergence remains virtually unexplored in southern South America. To help fill this knowledge gap, in this study we investigated the demographic history of Centris cineraria, a solitary bee mainly distributed in Patagonia. We used mitochondrial and nuclear markers and performed phylogeographical and dating analyses, adjusted spatio-temporal diffusion and species distribution models, and used Approximate Bayesian Computation to identify likely historical demographic scenarios. Our results revealed that during glacial periods the Andes represented a barrier due to the extent of the ice-sheets and the occurrence of unsuitable habitats, while interglacials allowed for gene flow across the Andes. Secondary contact between previously isolated lineages was evident across at least two low-altitude Andean areas, the northern one being a putative glacial refugium. Our findings also suggest that C. cineraria has persisted in situ in four periglacial refugia located along a north–south transect, congruent with the maximum extent of the ice sheet during the Greatest Patagonian Glaciation. As the first phylogeographical study of Patagonian insects, our work reveals that the interaction between Quaternary climatic oscillations and the Andes as a barrier was the main driver of the spatial and demographic history of C. cineraria.

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Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz077 ◽

2019 ◽

Vol 128 (1) ◽

pp. 149-169 ◽

Cited By ~ 2

Author(s):

Drew R Schield ◽

Blair W Perry ◽

Richard H Adams ◽

Daren C Card ◽

Tereza Jezkova ◽

...

Keyword(s):

Gene Flow ◽

Demographic History ◽

Secondary Contact ◽

Tree Model ◽

Crotalus Viridis ◽

Species Complexes ◽

Isolating Mechanisms ◽

Allopatric Divergence ◽

History Of ◽

Study Population

Abstract The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.

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Reconstructing the demographic history of Atlantic Salmon (Salmo salar) across its distribution range using Approximate Bayesian Computations

10.1101/142372 ◽

2017 ◽

Cited By ~ 1

Author(s):

Quentin Rougemont ◽

Louis Bernatchez

Keyword(s):

North America ◽

Atlantic Salmon ◽

Northern Hemisphere ◽

Demographic History ◽

Secondary Contact ◽

Population Divergence ◽

Isolated Populations ◽

Quaternary Period ◽

History Of ◽

Approximate Bayesian

AbstractUnderstanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. In the Northern hemisphere in particular, species genetic makeup has been largely influenced by severe climatic oscillations of the Quaternary Period. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from 77 sampling sites from North America and Eurasia genotyped at 4,656 SNPs. By combining results from admixture graphs, geogenetic maps and an approximate Bayesian computation framework, we validate previous hypotheses pertaining to secondary contact between European and Northern American populations, but also demonstrate that European populations from different glacial refugia have been exchanging alleles in contemporary times. We further identify the major sources of admixture from the southern range of North America to more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire American range. Results also point to a role for linked selection in the form of background selection and or positive hitchhiking. Altogether, differential introgression and linked selective effects likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere Therefore we conclude that such heterogeneity among loci should be systematically integrated into demographic inferences of the divergence process, even between incompletely reproductively isolated populations.

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Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

Genetics Selection Evolution ◽

10.1186/s12711-021-00627-0 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Fan Jiang ◽

Ruiyi Lin ◽

Changyi Xiao ◽

Tanghui Xie ◽

Yaoxin Jiang ◽

...

Keyword(s):

Gene Flow ◽

South Asia ◽

South Asian ◽

Demographic History ◽

Nervous System Development ◽

Chromosome 1 ◽

Whole Genome ◽

Chinese Populations ◽

Asian Populations ◽

History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

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The Genetic History of France

10.1101/712497 ◽

2019 ◽

Author(s):

Aude Saint Pierre ◽

Joanna Giemza ◽

Matilde Karakachoff ◽

Isabel Alves ◽

Philippe Amouyel ◽

...

Keyword(s):

Genetic Structure ◽

Demographic History ◽

Migration Routes ◽

Effective Population ◽

Genetic Studies ◽

Independent Population ◽

Genome Wide Data ◽

Population Sizes ◽

History Of ◽

Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

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Population structure and demographic history of the chukar partridge Alectoris chukar in China

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

Author(s):

Sen Song ◽

Shijie Bao ◽

Ying Wang ◽

Xinkang Bao ◽

Bei An ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North America ◽

Demographic History ◽

Population Expansion ◽

Northwest China ◽

Population History ◽

Extant Species ◽

History Of ◽

Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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

Journal of Evolutionary Biology ◽

10.1111/j.1420-9101.2010.02186.x ◽

2010 ◽

Vol 24 (3) ◽

pp. 505-517 ◽

Cited By ~ 12

Author(s):

Z. M. HU ◽

W. LI ◽

J. J. LI ◽

D. L. DUAN

Keyword(s):

Gene Flow ◽

North Atlantic ◽

Demographic History ◽

Chondrus Crispus ◽

Spatial Expansion ◽

The North ◽

Irish Moss ◽

History Of ◽

The North Atlantic

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Diabolical survival in Death Valley: recent pupfish colonization, gene flow and genetic assimilation in the smallest species range on earth

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.2334 ◽

2016 ◽

Vol 283 (1823) ◽

pp. 20152334 ◽

Cited By ~ 46

Author(s):

Christopher H. Martin ◽

Jacob E. Crawford ◽

Bruce J. Turner ◽

Lee H. Simons

Keyword(s):

Gene Flow ◽

Demographic History ◽

Genetic Assimilation ◽

Death Valley ◽

Court Case ◽

Devils Hole ◽

Supreme Court Case ◽

History Of ◽

New Perspective ◽

Outstanding Question

One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis , survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 US Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of over 13 000 loci to infer the demographic history of pupfishes in Death Valley. Instead of relicts isolated 2–3 Myr ago throughout repeated flooding of the entire region by inland seas as currently believed, we present evidence for frequent gene flow among Death Valley pupfish species and divergence after the most recent flooding 13 kyr ago. We estimate that Devils Hole was colonized by pupfish between 105 and 830 years ago, followed by genetic assimilation of pelvic fin loss and recent gene flow into neighbouring spring systems. Our results provide a new perspective on an iconic endangered species using the latest population genomic methods and support an emerging consensus that timescales for speciation are overestimated in many groups of rapidly evolving species.

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