Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora (original) (raw)
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Ecology and Evolution
Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai-Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well-differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.
Rethinking the Palearctic-Oriental Biogeographic Boundary in Quaternary China
This paper reviews the Chinese Quaternary biogeographic record, which has traditionally been divided into the Palearctic (North China) and Oriental (South China) biozones. Notable findings are: (1) Open-steppe taxa (e.g., Equus sanmeniensis, E. yunnanensis, E. hemonius, Mammuthus) are found in the Oriental region during the Early and Late Pleistocene; (2) Beremendia is found in large numbers at the Early Pleistocene Renzidong site located in the Oriental region, though it had previously been known only from the Palearctic biozone; (3) Oriental taxa are found in Middle Pleistocene deposits in northern China, though an increase in the winter monsoon intensity after 520 ka probably forced many of the warm climate taxa back southwards; (4) A higher number of primate taxa is present in the Oriental region, increasing in species diversity from the Early Pleistocene to the Holocene; and (5) Most of central-east China is less than 1,000 m above sea level and served as a continuous migration corridor between the Palearctic and Oriental biogeographic zones during the Quaternary. The general conclusion that we draw from this brief review is that the utility of a strict division between the Palearctic and Oriental biogeographic zones is not valid. In light of fluctuating paleoenvironmental pressures, Palearctic faunas often migrated southward during stadials and Oriental taxa were able to expand northward during interstadials. More detailed reconstructions of the eastern Asian biogeographic record, along with linking the data to the loess-soil, deep sea oxygen isotope, paleobathymetric, and pollen records, will facilitate a deeper understanding of how the paleoenvironment influenced hominin dispersals and evolution during the Quaternary.
Phylogeographic studies of plants in China: Advances in the past and directions in the future
Journal of Systematics and Evolution, 2012
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.
Quaternary history of the temperate forests of China
Quaternary Science Reviews, 1988
Pollen data from 80 sites in North China and Northeast China are reviewed to document the Quaternary history of the deciduous forest and the temperate mixed conifer-hardwood forest of China. During the Late Tertiary the forest in North China consisted of an admixture of temperate deciduous hardwoods, subtropical broadleaved evergreen elements, and ancient conifers of tropical and subtropical affinities. Pollen evidence from long boreholes through Quaternary deposits indicates four or five glacial/interglacial climatic cycles. The first glacial episode, known as the Nangou Cold Period, led to the development of a spruce-fir forest of no modern analogue in North China. Deciduous forest was re-established in North China during the intervening interglacials. The subtropical evergreen elements and Tertiary relicts were successively eliminated during the subsequent glacials. In the last glacial, spruce-fir forests which are now confined to mountain slopes above 1500 m descended to the lowlands of North and Northeast China, implying a temperature depression of at least 8-10°C. Cold steppe occurred at least locally near Beijing in the last glacial maximum, but the data base is insufficient to delimit the spatial and temporal extent of this and other paleovegetation types on a regional scale, or to reconstruct the locations of glacial refugia and the dynamics of plant migration. The Holocene pollen stratigraphies suggest a tripartite division, with a period of maximum warmth, the Hypsithermal, in the mid-Holocene. In both North and Northeast China, the forest became more diverse during the mid-Holocene when thermophilous hardwoods expanded at the expense of pine and, in more southerly locations, birch. Unequivocal evidence for intensified summer monsoon during the early Holocene, as predicted by the Kutzbach model based on orbital parameter changes, remains to be found from the pollen records of the temperate forest regions of China.
Historical geoclimatic events have shaped the distribution patterns and intraspecific divergence of plants. Numerous phylogeographical studies in China have focused on the Qinghai-Tibetan Plateau and surrounding areas due to the complex topography and high species diversity, but the impact of Neogene events and Quaternary climatic change on the flora of subtropical China remains poorly understood. Quercus glauca, a widespread tree of East Asian subtropical evergreen forests, has rich fossil records dating back to the Neogene, and it provides a good model to explore the impact of paleogeoclimate changes on East Asian subtropical forests. We used three chloroplast DNA (cpDNA) intergenic spacer regions and ecological niche modeling (ENM) to analyze the divergence pattern and demographic history of Q. glauca in China and Japan. A total of 33 haplotypes were detected. The phylogenetic analysis revealed two major haplotype lineages (Southwest China vs. Southeast China and East China Sea). The limited dispersal ability of seeds and complex topography resulted in the high total, inter-and intrapopulation haplotype diversity. The fossil-constrained BEAST analysis revealed a lineage diversification in the late Miocene-Pliocene. The formation of complex topography changes since Miocene in east Himalaya and adjacent area might be the key factor that triggered the intraspecific divergence of Q. glauca. Haplotype spatial distribution, ENM, mismatch distribution, and neutrality tests suggest that Q. glauca in Southeast China experiences expansion, and the current distribution in region III might be shaped by southward expansion from regions I and II after last glacial maximum (LGM). Regions I and II were the potential glacial refugia of Q. glauca.
Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau
Frontiers in genetics, 2014
The Qinghai-Tibetan Plateau (QTP) is the highest and one of the most extensive plateaus in the world. Phylogenetic, phylogeographic, and ecological studies support plant diversifications on the QTP through multiple mechanisms such as allopatric speciation via geographic isolation, climatic oscillations and divergences, pollinator-mediated isolation, diploid hybridization and introgression, and allopolyploidy. These mechanisms have driven spectacular radiations and/or species diversifications in various groups of plants such as Pedicularis L., Saussurea DC., Rhododendron L., Primula L., Meconopsis Vig., Rhodiola L., and many lineages of gymnosperms. Nevertheless, much work is needed toward understanding the evolutionary mechanisms of plant diversifications on the QTP. Well-sampled biogeographic analyses of the QTP plants in the broad framework of the Northern Hemisphere as well as the Southern Hemisphere are still relatively few and should be encouraged in the next decade. This paper...
Molecular Phylogenetics and Evolution, 2009
To explore the evolutionary consequences of climate-induced fluctuations in presently fragmented temperate forest habitats in continental East Asia we investigated the phylogeography and demographic history of the temperate-deciduous forest endemic Dysosma versipellis from disjunct montane sites in Central-Southeast China. Based on a survey of chloroplast (cp) DNA sequence variation, our analyses show that this perennial herb consists of morphologically indistinguishable western and central/eastern cpDNA lineages. Coalescent analyses under the 'isolation with migration' (IM) model support an ancient (Mid-Pleistocene) divergence between these lineages, with the western lineage having persisted without significant population growth in a long-term refuge just east of the Tibetan (Qinghai-Xizang) Plateau. In contrast, for the central/eastern lineage, we found strong evidence for population expansion from a refuge located south of the middle and lower reaches of the Yangtze River, and likely coinciding with the last or penultimate interglacial, followed by considerable population isolation and divergence in situ over (at least) the latest glacial-interglacial cycle. In line with recent evidence from palaeomodeling of East Asian forest biomes, our results suggest that the same vicariance factor, i.e. climate-induced eco-geographic isolation through (a)biotic displacement of temperate-deciduous forested habitats, promoted the divergence of D. versipellis lineages and populations at different spatial-temporal scales and over glacial and interglacial periods. Thus, there is no evidence that populations of D. versipellis merged at lower elevations during the last glacial(s). As such, D. versipellis accords with the premise that Late Quaternary refugial isolation is likely to have enhanced allopatric (incipient) species formation of temperate plants in East Asia.