Pleistocene glaciations, demographic expansion and subsequent isolation promoted morphological heterogeneity: A phylogeographic study of the alpine Rosa sericea complex (Rosaceae) (original) (raw)
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The aim of the present study was to investigate the phylogeographic patterns of Spiraea alpina (Rosaceae) and clarify its response to past climatic changes in the climate-sensitive Qinghai-Tibetan Plateau (QTP). We se-quenced a chloroplast DNA fragment (trnL–trnF) from 528 individuals representing 43 populations. We identified 10 haplotypes, which were tentatively divided into three groups. These haplotypes or groups were distributed in the different regions of the QTP. Only half the populations were fixed by a single haplotype, whereas the others contained two or more. In the central and eastern regions, adjacent populations at the local scale shared the same haplotype. Our phylogeographic analyses suggest that this alpine shrub survived in multiple refugia during the Last Glacial Maximum and that earlier glaciations may have trigged deep intraspecific divergences. Post-glacial expansions occurred only within populations or across multiple populations within a local range. The findings of the present study together with previous phylogeographic reports suggest that evolutionary histories of plants in the QTP are complex and variable depending on the species investigated.
Heredity, 2015
Arctic-alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic-alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north-south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic-alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.
Journal of Integrative Plant Biology, 2009
To date, little is still known about how alpine species occurring in the Qinghai-Tibetan Plateau (QTP) responded to past climatic oscillations. Here, by using variations of the chloroplast trnT-L, we examined the genetic distribution pattern of 101 individuals of Potentilla glabra, comprising both the interior QTP and the plateau edge. Phylogenetic and network analyses of 31 recovered haplotypes identified three tentative clades (A, B and C). Analysis of molecular variance (AMOVA) revealed that most of the genetic variability was found within populations (0.693), while differentiations between populations were obviously distinct (F st = 0.307). Two independent range expansions within clades A and B occurring at approximately 316 and 201 thousand years ago (kya) were recovered from the hierarchical mismatch analysis, and these two expansions were also confirmed by Fu's F S values and 'g' tests. However, distant distributions of clade C and private haplotypes from clades A and B suggest that they had survived the Last Glacial Maximum (LGM) and previous glaciers in situ since their origins. Our findings based on available limited samples support that multiple refugia of a few cold-enduring species had been maintained in the QTP platform during LGM and/or previous glacial stages. JQ (2009). Repeated range expansion and glacial endurance of Potentilla glabra (Rosaceae) in the Qinghai-Tibetan Plateau.
Molecular Phylogenetics and Evolution, 2011
The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-) temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences of the main phylogeographic findings in light of palaeo-environmental evidence, emphasize notable gaps in our knowledge, and outline future research prospects for disentangling the evolution and biogeographic history of the region's extremely diverse temperate flora.
Heredity, 2009
The Qinghai-Tibetan Plateau is one of the most extensive habitats for alpine plants in the world. Therefore, the patterns of genetic variation in populations on the Plateau can reveal the detailed demographic history of alpine plants. We analysed the geographical structure of chloroplast matK sequence variation in Potentilla fruticosa L. (Rosaceae), a shrub currently found across the entire Plateau. We obtained sequence data from 508 individuals from 23 populations at sites ranging from the high-altitude interior to the relatively low-altitude northeastern Plateau. In the interior region, genetic diversity was high and included ancestral haplotypes. In contrast, northeastern populations were characterized by relatively low genetic diversity and recently derived haplotypes. The estimated expansion time in the interior population was 17 times that in the northeastern population. These data suggest that P. fruticosa expanded its range on the Plateau during periods of climatic cooling and contracted to the interior region during warmer periods. Thus, the interior region acted as a refugium and greatly contributed to the diversification of P. fruticosa.
The genetic structure and phylogeographical history of the alpine shrubs Sibiraea angustata (Rosaceae) and Sibiraea laevigata from the QinghaieTibetan Plateau (QTP) were investigated to identify alpine plant responses to changes in the QTP and glaciations. Fifty-five populations were analyzed using four chloroplast DNA (cpDNA) regions and (nuclear ri-bosomal internal transcribed spacer) nrITS sequence data. In all, 21 cpDNA haplotypes and 13 nrITS sequence types were detected. Analyses of the genetic diversity and phylogenetic relationships detected two rarely reported glacial refugia. One was the YushueNangqian area, and the other consisted of the area from the Songpan Plateau to the southeastern margin of the QTP. Sibiraea species populations experienced divergent evolution and founder effects when they recolonized the QTP platform and adjacent high-altitude regions following glaciations. The divergence times of the main lineages and haplotypes were in the range of 1.60e2.58 Ma. The population size of Sibiraea species in the QTP decreased approximately 23-fold during the last 0.12 Ma, indicating that Sibiraea species were significantly affected by environmental changes in the QTP. Therefore, the rapid uplift of the QTP and subsequent glaciations likely played an important role in driving genetic divergence and population size changes of Sibiraea species in the QTP.
The Qinghai-Tibetan plateau (QTP) uplift had a decisive effect on climatic and eco-environmental evolution in East Asia during the Quaternary. In the current study phylo-geographic structure and diversification history of Spiraea alpina across the QTP were investigated for the first time based on nuclear internal transcribed spacer. The nuclear internal transcribed spacers (ITS 1a eITS 4) were generated for a total of 284 individuals distributed within 31 natural populations. A clear phylogeographic structure was found for S. alpina. The results showed that this species colonized in three different glacial refugia during the Quaternary extensive glaciation and expanded during the Interglacial period. Analysis of molecular variance (AMOVA) showed 74.13% genetic diversity among populations and 25.87% genetic variation within populations with distinct phylogeographic structure (F ST ¼ 0.741*). The estimated divergence time revealed that the main lineages of S. alpina diversified during the Quaternary 1.2e0.6 million years ago. The study concluded that severe climatic oscillations during Quaternary and the uplift of QTP had a profound effect on intraspecific divergence of S. alpina.
Molecular Ecology, 2009
Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20-rps12 intergenic spacer, the trnV intron and psbA-trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species' range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east-west split of cpDNA divergence was supported by an AMOVA which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the 'four-refugia' hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south-eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold-tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.
Biological Journal of the Linnean Society, 2011
Increasing evidence suggests that geological or climatic events in the past promoted allopatric speciation of alpine plants in the Qinghai-Tibetan Plateau and adjacent region. However, few studies have been undertaken to examine whether such allopatric divergences also occurred within a morphologically uniform species. In the present study, we report the evolutionary history of an alpine shrub species, Hippophae tibetana, based on examining chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variations. We sequenced two cpDNA fragments (trnL-F and trnS-G) and the nuclear ITS region in 183 individuals collected from 21 natural populations. Ten chlorotypes and 17 ITS types were identified. Phylogenetic analyses of both chlorotypes and ITS sequence variations suggested two distinct lineages distributed in the eastern and western region, respectively. On the basis of the fast and low plant substitution rates, these two lineages were estimated to have diverged from each other between 1 and 4 million years ago, during the period of the major glaciations and orogenic processes. In addition, ITS has undergone the accelerated evolution in two populations in the southern Himalaya isolated by the high mountains with a surprising accumulation of the private variations. The east-west split was also supported by an analysis of molecular variance, which partitioned around 91% of the total cpDNA variance between these two groups of populations. A single chlorotype was found for most populations in eastern or western region, suggesting a recent postglacial expansion within each region. Star-phylogeny and mismatch analyses of all chlorotypes within the eastern group of populations suggested an earlier regional expansion before the Last Glacial Maximum (LGM). The local fixture of the different chlorotypes in multiple populations suggested more than one refugia remained for eastern or western region. Coalescent tests rejected the hypothesis that all current populations originated from a single refugium during the LGM. Instead, they supported hypothesis that two lineages diverged before the late Pleistocene. These findings, when taken together, suggested that this species had experienced long allopatric divergence and recent regional range expansions in response to orogenic processes and the climate changes. The evolutionary history of this shrub species highlights importance of geographical isolations to the intraspecific divergence of alpine plants occurring in the world's ruff.
Phylogeography of Potentilla fruticosa, an alpine shrub on the Qinghai-Tibetan Plateau
Journal of Plant Ecology, 2009
Aims Our objectives were (i) to elucidate the phylogeography of chloroplast DNA (cpDNA) in Potentilla fruticosa in relation to Quaternary climate change and postglacial colonization, (ii) to infer historical population range expansion using mismatch distribution analyses and (iii) to locate the refugia of this alpine species on the Qinghai-Tibetan plateau during glacial-interglacial periods. Methods Potentilla fruticosa is a widespread species distributed on the Qinghai-Tibetan Plateau. We sampled leaves of P. fruticosa from 10 locations along a route of ;1 300 km from the northeastern plateau (Haibei, Qinghai) to the southern plateau (Dangxiong, Tibet). We examined the cpDNA of 15 haplotypes for 87 individuals from the 10 populations based on the sequence data from ;1 000 base pairs of the trnS-trnG and rpl20-rps12. Phylogenetic relationship of haplotypes was analyzed using the Phylip software package and the program TCS. The diversity of populations indices was obtained using the program ARLEQUIN. Important Findings With the limited samples, we found that (i) higher nucleotide diversity often occurs in high-altitude populations, (ii) the ancestral haplotypes distribute in the populations with higher nucleotide diversity than recent haplotypes, (iii) the expansion time of population in the high altitudes was estimated to be approximately at 52-25 ka BP (1000 years Before Present, where ''Present'' is AD 1950) and that in the low altitudes to be ;5.1-2.5 ka BP and (iv) the source location of P. fruticosa is at the high altitudes, which might provide refugia for the species during the interglacial warm periods. The species expanded from the high-elevated locations on the Tanggula Mountains during the Holocene. Keywords: alpine plants d climatic changes d cpDNA d Qinghai d Tibet