RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae) (original) (raw)
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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.
Biological Journal of the Linnean Society, 2014
Given that East Asia is located southwest of Beringia and was less glaciated during the Pleistocene, species at higher latitudes were able to expand their range in this region during climate cooling. Although southward migration is an inevitable colonization process, the biogeographical history of the disjunct ranges of higher-latitude species in East Asia has been investigated less extensively. Here, we assess whether their disjunct distributions in the Japanese archipelago connected sufficiently with Beringia or persisted in isolation following their establishment. Sequences of nine nuclear loci were determined for Cassiope lycopodioides (Ericaceae) from the Japanese archipelago as well as its surrounding areas, Kamchatka and Alaska. According to the geographical pattern of genetic diversity, the northern populations from Kamchatka to the northern part of the Japanese archipelago were similar genetically and were differentiated from populations in central Japan. Our study suggested that the distribution of C. lycopodioides was connected between the northern part of the Japanese archipelago and southwestern Beringia due to Pleistocene climate cooling. Conversely, central Japan harboured a disjunct range after its establishment. These inferences suggest that widespread range expansion in northern East Asia was plausible for species distributed in Beringia.
Biological Journal of the Linnean Society, 2009
According to previous phylogeographic studies, high mountains at low latitudes are important areas for the study of the evolutionary history of arctic-alpine plants in surviving the Pleistocene climatic oscillations. To evaluate this hypothesis, we elucidated the genetic structure of the arctic-alpine plant, Loiseleuria procumbens, in the Japanese archipelago, which corresponds to one of the southernmost limits of its distribution, using 152 individuals from 17 populations that covered the entire distribution of the Japanese archipelago and Sakhalin, in addition to samples from Sweden. Based on 854 bp of chloroplast DNA, we detected eight haplotypes. Along with haplotype distribution, strong genetic differentiation between populations in central and northern Japan was elucidated by a neighbour-joining tree (100%) and spatial analysis of molecular variance (79%), which is consistent with other alpine plants in Japan, regardless of the species' range. In addition, the southernmost populations from northern Japan showed specific genetic structure, although the remaining areas of northern Japan and Sakhalin harboured an homogenous genetic structure. Our results suggest that the populations in central Japan persisted for a long time during the Pleistocene climatic oscillation and that genetic divergence occurred in situ, supporting our hypothesis in conjunction with a previous study of another arctic-alpine plant, Diapensia lapponica subsp. obovata.
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.
Biological Journal of the Linnean Society, 2013
Discordant phylogeographical patterns among species with similar distributions may not only denote specific biogeographical histories of different species, but also could represent stochastic variance of genealogies in applied genetic markers. A multilocus investigation representing different genomes can be used to address the latter concern, allowing robust inference to biogeographical history. In the present study, we conducted a multilocus phylogeographical analysis to reexamine the genetic structuring of Phyllodoce nipponica, in which chloroplast (cp)DNA markers exhibited a discordant pattern compared to those of other alpine plants. The geographical structure of sequence variation at five nuclear loci was not consistent with that of cpDNA and showed differentiation between the northern and southern parts of the range of this species. Its demographic history inferred from the isolation-withmigration model suggests that the north-south divergence originated from Pleistocene vicariance. In addition, the demographic parameters showed a lack of chloroplast-specific gene flow, suggesting that stochastic variance in genealogy resulted in the discordant geographical structure. Thus, P. nipponica probably experienced Pleistocene vicariance between its southern and northern range parts in concordance with other alpine plants in the Japanese archipelago. The findings of the present study demonstrates the importance of using a multilocus approach for inferring population dynamics, as well as for reconciling discordant phylogeographical patterns among species.
Molecular phylogeny and biogeography of the arctic-alpine genus Lagotis (Plantaginaceae)
Taxon, 2014
It has been suggested that many plants now found in the arctic originated from ancestors that occurred at high altitudes in the southern mountains of the Northern Hemisphere during the Tertiary. However, this hypothesis has rarely been tested using a molecular phylogenetic approach. Here, we present a fossil-calibrated molecular phylogeny of Lagotis, an arctic-alpine genus with the greatest diversity in the Qinghai-Tibetan Plateau (QTP) and Central Asian mountains, based on five chloroplast (matK, psbA-trnH, rps16, trnG-S, trnL-F) and nuclear ribosomal ITS DNA markers. Within this framework, we infer the ancestral area and biogeographic history of the genus. Four major clades (A-D) within Lagotis were recovered with strong support, which largely correspond to the previous classification of the genus. Within clade A, Lagotis species from QTP were distributed among several subclades, and L. integrifolia from Central Asia was sister to L. glauca and L. minor from the arctic and subarctic region. The Bayesian molecular dating and the ancestral area reconstruction analyses suggested that Lagotis could have originated in the QTP in the Miocene (Tertiary), and that the genus radiated from the Miocene to Pleistocene. The diversification of Lagotis probably took place predominantly in the QTP and it subsequently spread to the Central Asian highlands, followed by northward migration into the arctic. Our results support the hypothesis that the "Central Asiatic Highland Corridor" as an important route for the migration of the flora between the arctic and QTP. ) and alignment are available in the Supplementary Data section of the online version of this article at
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.
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