Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China

Gp, Ren; Rj, Abbott; Zhou, Yongfeng; Lr, Zhang; Yl, Peng; Jq, Liu

doi:10.1038/hdy.2011.123

Cited by 36 publications

(30 citation statements)

References 64 publications

(89 reference statements)

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“…The pattern of rapid population growth in the Middle-Late Pleistocene predating the Last Glacial Maximum (LGM, 26.5-19 ka) could be explained by increasing aquatic habitats after the largest Quaternary glaciation in the Middle Pleistocene recorded in the East Asia (Zheng et al, 2002;Wu et al, 2002). Our findings add to a growing body of evidence suggesting recent population growth in the Middle-Late Pleistocene prior to the LGM, as found in freshwater fishes (e.g., Watanabe et al, 2010) and terrestrial organisms from East Asia (e.g., Ding et al, 2011;Ren et al, 2012).…”

Section: Glacial Refugia and Pleistocene Split Of Major Cladesmentioning

confidence: 63%

Phylogeographical Analysis of a Cold-Temperate Freshwater Fish, the Amur Sleeper (Perccottus glenii) in the Amur and Liaohe River Basins of Northeast Asia

Wang

Yin²,

Chen³

et al. 2014

Zoological Science

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The Amur sleeper Perccottus glenii (Perciformes, Gobioidei, Odontobutidae) is well known as an invasive fish in the river basins of Eastern and Central Europe, but its genetic background is unavailable across its native habitats in northeast Asia. In this study, we used the mitochondrial cytochrome b gene by sampling 19 populations of P. glenii across its native distributional areas of Liaohe and Amur River basins to explore its evolutionary history. Phylogenetic analyses identified three major clades within P. glenii, among which Clade A and Clade B were co-distributed in the Liaohe and Amur River basins, and Clade C was restricted to the latter. Molecular dating showed that the splits of Clades A, B and C have happened in the late Early-early Middle Pleistocene and the most recent common ancestors of these clades have been presented in the late Middle-early Late Pleistocene. The P. glenii showed very high levels of genetic structure among populations (ΦST = 0.801), probably due to the characters of its life histories with very limited dispersal ability. The admixture of different clades in some populations of P. glenii probably reflects historical secondary contact. These findings indicate that Pleistocene climatic oscillation and river capture were major determinants for genetic variations and evolutionary history of the P. glenii.

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Section: Glacial Refugia and Pleistocene Split Of Major Cladesmentioning

confidence: 63%

Phylogeographical Analysis of a Cold-Temperate Freshwater Fish, the Amur Sleeper (Perccottus glenii) in the Amur and Liaohe River Basins of Northeast Asia

Wang

Yin²,

Chen³

et al. 2014

Zoological Science

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“…Similarly in northern and northeast China, phylogeographic studies suggest regional expansions and multiple glacial refugia for a limited number of species with glacial refugia being sparsely located in the mountains from the north to the south (e.g., Chen et al, 2008a; Du et al, 2009; Tian et al, 2009; Bai et al, 2010; Guo et al, 2010; Ren et al, 2011; Zeng et al, 2011; An et al, 2012). However, in middle, southern and southeast China, regional expansions were found rarely and only local expansions occurred in the studied species (e.g., Su et al, 2005; Wang & Ge, 2006; Gao et al, 2007; Yan et al, 2007; Qiu et al, 2009a, 2009b; Wang et al, 2009a; Zhou et al, 2010; Chen et al, 2012; Li et al, 2012c; Peng et al, 2012; Xiao et al, 2012; Xie et al, 2012).…”

Section: Phylogeographic Patterns Of Plants In Chinamentioning

confidence: 99%

Phylogeographic studies of plants in China: Advances in the past and directions in the future

Liu

Sun

et al. 2012

J of Sytematics Evolution

220

267

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Phylogeography has been one major focus of evolutionary biology in recent years, with many important advances in Chinese species. In this issue, we collected 11 phylogeographic studies of plants by Chinese laboratories. We further synthesized the main findings and patterns emerging from these and previous phylogeographic studies in China and asked where phylogeographic research should be directed in the coming years. Numerous examples have shown that phylogeographic patterns in China did not show an expected expansion-contraction pattern at large scale, mirroring the geological records showing that no unified ice sheet had developed in China during the Quaternary Period. Instead, regional expansions and intraspecific divergences are very common in most studied species during the Quaternary oscillations. Different intraspecific lineages or alleles (haplotypes) were detected in multiple localized refugia, from where regional or local expansions are likely to have started. Hybridizations and introgressions are frequent between intraspecific lineages or between different species. We also reviewed computational methods for phylogeographic analyses. Despite the great progress made in recent years, there remains much to discover about the spatial-temporal dimensions and underlying speciation mechanisms of Chinese plants. Phylogeographic studies represent a key knot that connects the genus phylogeny (macroevolution) and speciation and adaptation (microevolution). Therefore, we advocate that: (i) phylogeographic studies of plants in China should be directed to the closely related species or a monophyletic group (for example, a genus or a section) in the coming years; and (ii) population genetic data based on direct sequencing multiple loci, especially those from nuclear genome and statistical tests should be widely adopted and enforced. The recovered intraspecific divergences and phylogeographic patterns of multiple-species may allow us to better understand the high plant diversity in China and set up concrete hypotheses for studying plant speciation and diversification mechanisms in this region.

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“…Some studies have indicated that positive selection might have been involved in the adaptation of Pinus species to shifts in environmental conditions during their evolutionary and speciation processes (Ma et al, ; Ruhfel et al, ; Zhou et al, ). This type of information can provide valuable genetic resources for investigating the adaptive population history and interspecific divergence of closely related species (Ren et al, ; Zhou et al, ).…”

Section: Introductionmentioning

confidence: 99%

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

Zeb

Dong

Zhang

et al. 2019

J of Sytematics Evolution

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Pinus L. is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms. However, our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny. Thus, we analyzed the sequences of 97 Pinus plastid genomes, including four newly sequenced genomes and 93 previously published plastomes, to explore the evolution and phylogenetic relationships in the genus Pinus. The complete chloroplast genomes of Pinus species ranged in size from 109 640 bp (P. cembra L.) to 121 976 bp (P. glabra Walter), and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms. We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983 (44%), followed by tandem repeats with 2999 (33%), and then palindromic repeats with 2126 (23%). Sixteen divergence hotspot regions were identified in Pinus plastid genomes, which could be useful molecular markers for future population genetics studies. Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus (single needle section) and Pinus (double needles section). Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous. The two subgenera subsequently split 85.86 Mya, which was largely consistent with the other molecular results based on partial DNA markers. These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.

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Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China

Cited by 36 publications

References 64 publications

Phylogeographical Analysis of a Cold-Temperate Freshwater Fish, the Amur Sleeper (Perccottus glenii) in the Amur and Liaohe River Basins of Northeast Asia

Phylogeographical Analysis of a Cold-Temperate Freshwater Fish, the Amur Sleeper (Perccottus glenii) in the Amur and Liaohe River Basins of Northeast Asia

Phylogeographic studies of plants in China: Advances in the past and directions in the future

Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships

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