Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree

Bai, Wei‐Ning; Wang, Wenting; Zhang, Dayong

doi:10.1016/j.ympev.2014.08.024

Cited by 68 publications

(66 citation statements)

References 81 publications

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“…Our simulations of the distributions of the I. bungeana complex during the LGM also indicated that the distribution did not migrate southward significantly although the core distributions shrank, which is also consistent with the species with similar distribution in East Asia, such as Juglans cathayensis 42 , Quercus variabilis 43 , and Tetrastigma hemsleyanum 44 .…”

Section: Discussionsupporting

confidence: 81%

The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

Zhao

Gao

Zhu

et al. 2017

Sci Rep

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East Asia harbors the highest level of floristic diversity among the world’s temperate regions. Despite the increase in phylogeographic studies of temperate plants in East Asia, far less attention has been paid to widely distributed deciduous shrubs that widespread across several floral regions. We sequenced two chloroplast DNA (cpDNA) fragments (ndhJ-trnF and trnD-trnT) and one nuclear DNA (Pgk1) of 472 individuals from 51 populations of such a group, the Indigofera bungeana complex. We used population genetic data as well as ecological niche modelling to examine the evolutionary history and glacial refugia during the Last Glacial Maximum (LGM) of this group. We recovered 133 cpDNA and 68 nuclear haplotypes. The star-phylogeny of the recovered cpDNA and nuclear haplotypes and demographic analyses suggested distinct range expansion of I. bungeana complex have occurred during the early and middle Pleistocene. The climate change of the LGM might have affected little on the distribution of this complex based on the niche modelling. However, these climate changes and geographic isolation probably resulted in fixtures of the private haplotypes and genetic differentiations between regions. Our results suggested that this arid-tolerant species complex may have different responses to the Quaternary climate changes with those climate-sensitive species.

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Section: Discussionsupporting

confidence: 81%

The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

Zhao

Gao

Zhu

et al. 2017

Sci Rep

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“…Seventeen pairs of microsatellite primers developed for Juglans nigra ( Juglans nigra L.) and Juglans cinerea ( Juglans cinerea L.) (Woeste et al ., ; Dangl et al ., ; Hoban et al ., ; Ross‐Davis & Woeste, ) were used to amplify and genotype all of the individuals using the method described in Bai et al . () (Table S2). One nuclear gene, LEAFY , was amplified and sequenced for 397 individuals from 44 populations (Table ), following the protocols of Yang et al .…”

Section: Methodsmentioning

confidence: 99%

Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia

2015

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Summary East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single‐copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate‐induced vicariance of an ancestral northern range during the mid‐Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north–south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.

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“…Moreover, the ‘refugia within refugia’ scenario as described by Gómez & Lunt () has recently been suggested for warm‐temperate plant species in subtropical China, although asymmetric gene flow via pollen and seed could result in a cytoplasmic‐nuclear discordance in the population structure (Bai et al . ).…”

Section: Introductionmentioning

confidence: 97%

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

et al. 2015

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In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool-temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial-interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high-latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.

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Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree

Cited by 68 publications

References 81 publications

The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

The demographic response of a deciduous shrub (the Indigofera bungeana complex, Fabaceae) to the Pleistocene climate changes in East Asia

Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia

Multiple glacial refugia for cool‐temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

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