Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast

Wang, Xuejing; Que, Pinjia; Heckel, Gerald; Hu, Junhua; Zhang, Xuecong; Chiang, Chung Yu; Zhang, Nan; Huang, Qin; Liu, Simin; Martinez, Jonathan; Pagani‐Núñez, Emilio; Dingle, Caroline; Leung, Yu Yan; Székely, Tamás; Zhang, Zhengwang; Liu, Yang

doi:10.1186/s12862-019-1449-5

Cited by 31 publications

(42 citation statements)

References 127 publications

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“…The increasing availability of population genomic data has led to a new understanding of speciation beyond the classical categorization of sympatric, allopatric, and parapatric modes [1]. The recently developed field of "speciation genomics" has revealed that speciation with gene flow, a phenomenon that was once thought to be highly unlikely [2], is common [3][4][5][6][7], including between extant and extinct taxa (reviewed in [8]). These revelations suggest that the individual is not the unit of isolation, and that there must be regions of isolation within the genome maintaining species boundaries.…”

Section: Introductionmentioning

confidence: 99%

Genomic differentiation across the speciation continuum in three hummingbird species pairs

Henderson

Brelsford

2020

BMC Evol Biol

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Background: The study of speciation has expanded with the increasing availability and affordability of highresolution genomic data. How the genome evolves throughout the process of divergence and which regions of the genome are responsible for causing and maintaining that divergence have been central questions in recent work. Here, we use three pairs of species from the recently diverged bee hummingbird clade to investigate differences in the genome at different stages of speciation, using divergence times as a proxy for the speciation continuum. Results: Population measures of relative differentiation between hybridizing species reveal that different chromosome types diverge at different stages of speciation. Using F ST as our relative measure of differentiation we found that the sex chromosome shows signs of divergence early in speciation. Next, small autosomes (microchromosomes) accumulate highly diverged genomic regions, while the large autosomes (macrochromosomes) accumulate genomic regions of divergence at a later stage of speciation. Conclusions: Our finding that genomic windows of elevated F ST accumulate on small autosomes earlier in speciation than on larger autosomes is counter to the prediction that F ST increases with size of chromosome (i.e. with decreased recombination rate), and is not represented when weighted average F ST per chromosome is compared with chromosome size. The results of this study suggest that multiple chromosome characteristics such as recombination rate and gene density combine to influence the genomic locations of signatures of divergence.

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Section: Introductionmentioning

confidence: 99%

Genomic differentiation across the speciation continuum in three hummingbird species pairs

Henderson

Brelsford

2020

BMC Evol Biol

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“…The insular subspecies formosanus forms its own lineage, which is restricted to Taiwan. This island was repeatedly connected to Chinese mainland during cold periods in the Pleistocene, including the last glacial (Li et al , 2010, Wang et al 2019), which could have allowed recurrent gene flow after an initial colonization. We only found signs of gene flow from Taiwan back to mainland China (into the torquatus group), but gene flow in the opposite direction might have been masked by the effects of genetic drift in the small island population.…”

Section: Discussionmentioning

confidence: 99%

Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

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Y²,

E³

et al. 2019

Preprint

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AimHistorical factors such as Pleistocene climate cycles and associated environmental changes have influenced the phylogeographic structure and demographic dynamics of many species. Resulting patterns not only depend on species’ life-history but also vary regionally. Consequently, different populations of species with large ranges over different biomes might have experienced divergent drivers of diversification and show different population histories. Such a representative species is the common pheasant Phasianus colchicus, an ecological generalist with a wide distribution in the Palearctic and at the edge of the Oriental region. We aimed at identifying distinct phylogeographic lineages of the common pheasant and investigating their evolutionary trajectories.Study locationAsiaMethodsWe used coalescent approaches to describe the phylogeographic structure and to reconstruct the spatio-temporal diversification and demographic history of the common pheasant based on a comprehensive geographic sampling of 265 individuals genotyped at seven nuclear and two mitochondrial loci.ResultsThe common pheasant diversified during the late Pleistocene into eight distinct evolutionary lineages which only partly correspond to traditional morphological groups. It originated at the edge of the Qinghai-Tibetan plateau and spread from there to East and Central Asia. Only the widely distributed genetically uniform lowland lineage of East Asia showed a recent range and population expansion, starting during last glacial. More phylogeographic structure was found elsewhere with lineages showing no signs of recent range expansions. One lineage of subtropical south-central China this is the result of long-term isolation in a climatically stable and topographically complex region. In others from arid Central Asia and China, demographic and range expansions were impeded by repeated population fragmentation during dry glacial and recent aridification. Given such a phylogeographic structure and demographic scenarios among lineages, we proposed split the range-wide common pheasant into three species.Main conclusionsSpatio-temporal phylogeographic frameworks of widespread species complexes such as the common pheasant provide valuable opportunities to identify regionally divergent drivers of diversification.

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“…WFPs breed exclusively in a restricted coastal range from Fujian to Guangxi, as well as Hainan Island in south-east China. KPs nest to the north of this range (Wang et al, 2019). Previous work examining mitochondrial DNA and microsatellite markers has shown that although KPs and WFPs are phenotypically well-differentiated (Kennerley et al, 2008; Rheindt et al, 2011), genetically, they lack differentiation.…”

Section: Introductionmentioning

confidence: 99%

“…Previous work examining mitochondrial DNA and microsatellite markers has shown that although KPs and WFPs are phenotypically well-differentiated (Kennerley et al, 2008; Rheindt et al, 2011), genetically, they lack differentiation. More extensive microsatellite genotyping and autosomal nuclear sequencing (Wang et al, 2019) as well as genome-wide SNP identification and genotyping (Sadanandan et al, 2019), however, showed KPs and WFPs are distinct and young lineages. The two lineages diverged around 0.6 Ma with evidence of bidirectional gene flow (Wang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds

et al. 2019

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Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the whitefaced (C. dealbatus) plovers, which differ in their phenotype, ecology and behavior, are two incipient species and parapatrically distributed in East Asia. Previous studies show evidence of genetic diversification with gene flow between the two plovers. Under this scenario, it is of great importance to explore the patterns of divergence at the genomic level and to determine whether specific regions are involved in reproductive isolation and local adaptation. Here we present the first population genomic analysis of the two incipient species based on the de novo Kentish plover reference genome and resequenced populations. We show that the two plover lineages are distinct in both nuclear and mitochondrial genomes. Using model-based coalescence analysis, we found that population sizes of Kentish plover increased whereas white-faced plovers declined during the Last Glaciation Period. Moreover, the two plovers diverged allopatrically, with gene flow occurring after secondary contact. This has resulted in low levels of genome-wide differentiation, although we found evidence of a few highly differentiated genomic regions in both the autosomes and the Z-chromosome. This study illustrates that incipient shorebird species with gene flow after secondary contact can exhibit discrete divergence at specific genomic regions and provides basis to further exploration on the genetic basis of relevant phenotypic traits.

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Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast

Cited by 31 publications

References 127 publications

Genomic differentiation across the speciation continuum in three hummingbird species pairs

Genomic differentiation across the speciation continuum in three hummingbird species pairs

Regionally divergent drivers of historical diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

Demographic Histories and Genome-Wide Patterns of Divergence in Incipient Species of Shorebirds

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