Population genetic structure and demography of Magnolia kobus: variety borealis is not supported genetically

Species delimitations by morphological and by genetic markers are not always congruent. Magnolia kobus consists of two morphologically different varieties, kobus and borealis. The latter variety is characterized by larger leaves than the former. For the conservation of M. kobus genetic resources in natural forests, the relationships between morphological and genetic variation should be clarified. We investigated variations in nuclear microsatellites, chloroplast DNA (cpDNA) sequences and leaf morphological traits in 23 populations of M. kobus over the range of species. Two genetically divergent lineages, northern and southern were detected and their geographical boundary was estimated to be at 39°N. The northern lineage consisted of two genetic clusters and a single cpDNA haplotype, while the southern one had multiple genetic clusters and cpDNA haplotypes. The northern lineage showed significantly lower genetic diversity than the southern. Approximate Bayesian computation indicated that the northern and southern lineages had experienced, respectively, population expansion and long-term stable population size. The divergence time between the two lineages was estimated to be 565,000 years ago and no signature of migration between the two lineages after divergence was detected. Ecological niche modeling showed that the potential distribution area in northern Japan at the last glacial maximum was very small. It is thus considered that the two lineages have experienced different population histories over several glacial-inter-glacial cycles. Individuals of populations in the central to northern part of Honshu on the Sea of Japan side and in Hokkaido had large leaf width and area. These leaf characteristics corresponded with those of variety borealis. However, the delimitation of the northern and southern lineages detected by genetic markers (39°N) was not congruent with that detected by leaf morphologies (36°N). It is therefore suggested that variety borealis is not supported genetically and the northern and southern lineages should be considered separately when identifying conservation units based not on morphology but on genetic markers.

     

Riding the Kuroshio Current: Stepping stone dispersal of the Okinawa tree lizard across the East Asian Island Arc

Aim

Located hundreds of kilometres offshore of continental mainland Asia, the extremely high level of land vertebrate endemism in the East Asian Island Arc provides an excellent opportunity to test hypotheses regarding biogeographic processes and speciation. In this study, we aim to test alternative explanations for lineage diversification (vicariance versus dispersal models), and further develop a temporal framework for diversification in our focal taxon, which is consistent with the known age of these islands. We achieve these tests by investigating the historical biogeography of the Okinawa tree lizard (Japalura polygonata), one of the few widely‐distributed reptiles across this archipelago.

Location

The East Asian Island Arc: (1) Central Ryukyu (Amami and Okinawa groups); (2) Southern Ryukyu (Miyako and Yaeyama groups); (3) Taiwan and adjacent islands.

Methods

A total of 246 tissues were sampled from 10 localities in the Ryukyu archipelago and 17 localities in Taiwan, covering the entire distributional range of this species, including all subspecies. DNA sequences of the mitochondrial cytochrome b, 16S ribosomal RNA, nuclear BACH‐1 and RAG‐1 genes (total: 4,684 bp) were obtained from these samples. We used maximum likelihood and Bayesian methods to infer phylogeny and divergence time, and used a model‐fitting method of biogeographical inference to estimate ancestral range evolution.

Results

Multiple lines of evidence combine to identify a general pattern of dispersal‐mediated diversification northward through the archipelago, following initial dispersal from Taiwan. These included (1) a phylogenetic estimate, revealing a sequential, south‐to‐north branching pattern; (2) ancestral range estimation, inferring multiple overseas dispersals and subsequent colonization of new landmasses; and (3) a reduction in genetic variation observed in successively‐diverging lineages, decreasing from Taiwan northward, towards more remote islands. These results provide strong statistical support for an interpretation of successive bouts of dispersal via the powerful, well‐documented, south‐to‐north Kuroshio Current. Estimation of divergence times suggests that most clades in southern Ryukyu and Taiwan diverged early, giving rise to lineages that have remained isolated, and that more recently‐diverged lineages then colonized northward to subsequently occupy the landmasses of the Central Ryukyu archipelago.

Main conclusions

Our general inference of biogeographic history in Japalura polygonata suggested that this species originated on Taiwan and the Yaeyama group, and arrived at its current distribution in Miyako, Okinawa, Toku and Amami islands by a series of stepping‐stone dispersals, which we report for the first time for a terrestrial vertebrate endemic to this region.     

Evolution of the Euphrasia transmorrisonensis complex (Orobanchaceae) in alpine areas of Taiwan

Aims To unravel isolation and differentiation of the genetic structure of the Euphrasia transmorrisonensis complex, a showy herb, among alpine regions of mountain peaks in subtropical Taiwan and to infer its evolutionary history. Location Alpine ecosystems of high‐montane regions of Taiwan. Methods Phylogenetic analyses of the trnL intron and the trnL–trnF intergenic spacer of chloroplast (cp) DNA, and the intertranscribed spacer (ITS) of nuclear ribosomal (nr) DNA between 18S and 26S were carried out on 18 populations of the E. transmorrisonensis complex in Taiwan. Results In total, 10 haplotypes for cpDNA and 14 haplotypes for nrDNA were detected. Three population groups located in the northern, north‐eastern, and south‐central regions of the Central Mountain Range (CMR) were revealed according to the frequencies of haplotypes and haplotype lineages of nrDNA. Balancing selection might have played a role in the evolution of Euphrasia in Taiwan. Main conclusions By integrating the spatial‐genetic patterns of cpDNA and nrDNA, two possible evolutionary histories of Euphrasia in Taiwan were inferred. The favourable hypotheses for interpreting the data suggest at least three origins of the E. transmorrisonensis complex in Taiwan, corresponding to each nuclear lineage in the northern (II), northern/north‐eastern (I), and central/southern regions (III) with subsequent hybridization between lineages I and II and lineages II and III. These lineage boundaries are strengthened by the finding that haplotypes of C derived from cpDNA were found in the geographical region of lineage II of nrDNA, while haplotypes of A derived from cpDNA were found in the region of lineage III of nrDNA. Thus, the origin of chloroplasts exclusive to lineages II and III supports their long‐term isolation from one another.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands,the Ryukyu Archipelago,Japan

Aim Phylogeographical patterns in the Ryukyu Archipelago have been explained primarily by landbridge formation and the opening of two straits in the Pliocene, namely the Tokara and Kerama gaps. These old straits have been considered to be the barriers most likely to determine genetic boundaries. To test this, we conducted a molecular analysis of the herb Ophiorrhiza japonica. We discuss the causes of and processes involved in its phylogeographical structure and explore aspects of island separation other than the duration of the straits to explain genetic boundaries at the gaps. Location Ryukyu Archipelago, Japan. Methods Plants were collected from 40 localities in the archipelago and vicinity. Non‐coding regions of chloroplast DNA were sequenced. The genealogical relationships among haplotypes were estimated using a statistical parsimony network. To examine the phylogeographical structure, we compared two parameters of population differentiation, namely G_ST and N_ST, and conducted correlation analysis of genetic and geographical distances. Genetic boundaries were identified using Monmonier’s maximum difference algorithm. To test vicariance–dispersal hypotheses, that is, vicariance after migration via the Pliocene landbridge or over‐sea dispersal in the Pleistocene, molecular dating analysis was conducted. Results A statistical parsimony network revealed that the haplotypes from the Ryukyu Archipelago and northwards coalesce to one ancestral haplotype in Taiwan. A clear phylogeographical structure was observed: plants within the same population and populations in geographical proximity were phylogenetically close. A genetic boundary was recognized across the Kerama Gap, but not across the Tokara Gap. Dating analysis suggested that population divergence across the Kerama Gap occurred in the early to late Pleistocene. Main conclusions The statistical parsimony network suggests migration from Taiwan and northward range expansion in the archipelago. Based on the divergence time, over‐sea dispersal in the Pleistocene is likely, although migration via a Pliocene landbridge is not totally rejected. Negligible genetic differentiation across the Tokara Gap suggests recent over‐sea dispersal, possibly facilitated by the small geographical width of the gap. Conversely, the large genetic differentiation across the Kerama Gap is probably explained by the large geographical distance across it. The past splitting of a landbridge would have had a significant influence on population differentiation after a certain geographical distance was reached.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Genetic consequences of glacial survival: the late Quaternary history of balsam poplar (Populus balsamifera L.) in North America

Aim Beringia, the unglaciated region encompassing the former Bering land bridge, as well as the land between the Lena and Mackenzie rivers, is recognized as an important refugium for arctic plants during the last ice age. Compelling palaeobotanical evidence also supports the presence of small populations of boreal trees within Beringia during the Last Glacial Maximum. The occurrence of balsam poplar (Populus balsamifera) in Beringia provides a unique opportunity to assess the implications of persistence in a refugium on present‐day genetic diversity for this boreal tree species. Location North America. Methods We sequenced three variable non‐coding regions of the chloroplast genome (cpDNA) from 40 widely distributed populations of balsam poplar across its North American range. We assessed patterns of genetic diversity, geographic structure and historical demography between glaciated and unglaciated regions of the balsam poplar’s range. We also utilized a coalescent model to test for divergence between regions. Results Levels of genetic diversity were consistently greater for populations at the southern margin (θ_W = 0.00122) than in the central (θ_W = 0.00086) or northern (θ_W = 0.00034) regions of the current distribution of balsam poplar, and diversity decreased with increasing latitude (R² = 0.49, P < 0.01). We detected low, but significant, structure (F_CT = 0.05, P = 0.05), among regions of P. balsamifera’s distribution. The cpDNA genealogy was shallow, however, showing an absence of highly differentiated chloroplast haplotypes. Coalescent analyses supported a model of divergence between the southern ice margin and the northern unglaciated region of balsam poplar’s distribution, but analyses of other regional comparisons did not converge. Main conclusions The palaeobotanical record supports the presence of a Beringian refugium for balsam poplar, but we were unable to definitively identify the presence of known refugial populations based on genetic data alone. Balsam poplar populations from Beringia are not a significant reservoir of cpDNA diversity today. Unique alleles that may have been present in the small, isolated populations that survived within Beringia were probably lost through genetic drift or swamped by post‐glacial, northward migration from populations south of the ice sheets.     

Natural hybridization of Yezo and Sakhalin spruce in central Hokkaido,revealed by DNA markers with contrasting modes of inheritance

Yezo spruce (Picea jezoensis var. jezoensis) and Sakhalin spruce (Picea glehnii) occur across Hokkaido and co‐occur in some forest habitats. This leads to the potential for natural hybridization between these two species, which has been shown to occur at low frequencies. The purpose of this study was to identify these hybrids and their possible mating patterns, using various Pinaceae DNA markers with different modes of inheritance. The markers used were maternally inherited mitochondrial DNA (mtDNA), paternally inherited chloroplast DNA (cpDNA) and biparentally inherited nuclear microsatellites (nSSRs). Seven putative natural hybrids, four artificially‐crossed F₁ hybrids, four parent plants from each species, and two artificially‐backcrossed hybrids of putative natural hybrids and their parents were analyzed using the diagnostic DNA markers developed in this study. We found Yezo spruce and Sakhalin spruce to be distinct (J and G types, respectively), and the modes of inheritance held true for the two species, as was previously reported to be the case in Pinaceae. Four of the seven putative natural hybrids harbored J‐type cpDNA, G‐type mtDNA and J/G‐type nSSRs, indicating that natural F₁ hybrids are likely to arise from a G (female) × J (male) crossing. One natural hybrid harbored G‐type cpDNA, J‐type mtDNA and J/G‐type nSSRs, which implies that hybrids produced by J (female) × G (male) crossings occur at low frequencies. The two remaining hybrids harbored J‐type cpDNA and mtDNA with either J/G or J/J‐type nSSRs, suggesting that they may be F₂ hybrids resulting from backcrossing between an F₁ hybrid and a Yezo spruce.     

Geographic structuring of chloroplast DNA genotypes inTiarella trifoliata (Saxifragaceae)

Tiarella trifoliata comprises varietieslaciniata, trifoliata, andunifoliata, and is distributed from southeastern Alaska to northern California. We analyzed restriction site variation of chloroplast DNA (cpDNA) using 23 endonucleases in 76 populations representing the entire geographic range of the species and the three recognized varieties. We also employed comparative restriction site mapping of PCR-amplified chloroplast DNA fragments using 16 restriction endonucleases. This species exhibits low cpDNA restriction site variation. No differentiation is evident among varieties of this species based on cpDNA data; some plants of each variety were characterized by each of the two major cpDNA types detected. The two major cpDNA clades, which differ by only a single restriction site mutation, are geographically structured. A northern clade comprises populations from Alaska to central Oregon; most populations analyzed from southern Oregon and California form a southern clade. Populations that possess the typical northern cpDNA type also occur disjunctly to the south at high elevations in the Siskiyou—Klamath Mountain area of southern Oregon and northern California. Conversely, the southern cpDNA type is found disjunctly to the north in the Olympic Peninsula of Washington. Both geographic areas characterized by disjunct cytoplasms are considered glacial refugia.Tiarella trifoliata joins two other species,Tolmiea menziesii andTellima grandiflora, in having well-demarcated northern and southern cpDNA lineages. All three species have similar life-history traits and geographic distributions. We suggest that glaciation may have played a major role in the formation of the cpDNA discontinuities present in these three taxa. The pronounced relationship between cpDNA variation and geographic distribution suggests the potential applicability of intraspecific phylogeography to plants via the analysis of intraspecific cpDNA variation. These three examples also join a rapidly growing data base which indicates that cytoplasms are often geographically structured within species and species complexes.     

The east‐west‐north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae)

Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east‐to‐west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the ‘tabula rasa’ hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west‐east vs. west‐north colonization may be as a result of ‘high density blocking’ effect.     

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. 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.     

Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient

Although adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of post‐glacial colonization routes in determining phenotypic variation along gradients has received little attention. Here, we used a hierarchical Q_ST–F_ST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life histories along a 1,700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages; however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The Q_ST estimates between the colonization routes were four times higher than F_ST, indicating a prominent role for natural selection. Q_ST within the colonization routes did not generally differ from F_ST, but we found temperature‐dependent adaptive divergence close to the contact zone. These results indicate that lineage‐specific variation can account for much of the adaptive divergence along a latitudinal gradient.     

Recent origin and adaptive diversification of <Emphasis Type="Italic">Ainsliaea</Emphasis> (Asteraceae) in the Ryukyu Islands: molecular phylogenetic inference using nuclear microsatellite markers

We investigated the phylogeny and phylogeography of four closely related Ainsliaea species (Asteraceae) on the continental Ryukyu Islands of eastern Asia, which consist of two flood-adapted “rheophyte” and two non-rheophyte (inland) species, based on 12 nuclear microsatellite loci. Phylogenetic analyses using 420 individuals from 26 populations showed that rheophytic A. linearis and A. oblonga are genetically distinct. Each species was clustered with the inland species that occur on the same islands, suggesting a different ancestry for the two rheophytes that evolved independently by local adaptation to flooded habitats. The results from the neighbor-joining clustering and principal coordinate analysis (PCoA) indicate that the southern populations of A. macroclinidioides are distinct lineages and ancestral to the northern populations as well as the other diverse species complex in the Ryukyus. These results suggest a pattern of colonization initially from the Asian mainland to the southern islands, followed by the northern islands via land bridges generated during the Quaternary glaciations. After isolation from southern populations, species radiation and regional differentiation within the northern clade occurred possibly via local adaptation and/or geographic isolation of the subdivided island bridge.     

Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia

Abstract The Acacia acuminata complex includes three taxa, A. acuminata ssp. acuminata, A. acuminata ssp. burkittii and A. oldfieldii, along with several informal variants of A. acuminata. It is widespread throughout southern Australia with the centre of diversity in south‐west Western Australia. Phylogeographical patterns in the complex were investigated using a nested clade analysis of cpDNA RFLPs from 25 populations in Western Australia. Except for A. oldfieldii that was clearly identified as a distinct entity, haplotypes were not restricted to sub‐specific taxa or variants within A. acuminata. There was significant association between phylogenetic position of many haplotypes and their geographical distribution. The fine‐scale phylogeographical patterns were complex but at deeper levels in the phylogeny there was evidence of divergence between two lineages. The pattern of shared haplotypes between lineages suggests retention of ancestral polymorphism as a result of incomplete lineage sorting. The divergence of these lineages is consistent with fragmentation caused by climatic instability during the Pleistocene.     

Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China

How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed‐dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3–4) and paternally inherited, pollen‐ and seed‐dispersed chloroplast DNA (cpDNA) (rpl16 and trnS‐trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G_ST = 0.738, N_ST = 0.771) indicating low levels of seed‐based gene flow and significant phylogeographical structure (N_ST > G_ST, P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north–central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north‐central part of the species’ range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north‐central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among‐population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.     

Evolutionary history of an alpine shrub Hippophae tibetana (Elaeagnaceae): allopatric divergence and regional expansion

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. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 37–50.     

Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Population divergence and gene flow are key processes in evolution and ecology. Model‐based analysis of genome‐wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome‐level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.     

Vicariant speciation due to 1.55 Ma isolation of the Ryukyu islands,Japan, based on geological and GenBank data

The Ryukyu island arc, originally a continental margin arc, separated from the Chinese continent by the rifting of the Okinawa trough, a process which began at 1.55 million years ago (Ma) and continues to the present. In addition, the Ryukyu arc was simultaneously divided into the northern Amami–Okinawa and southern Yaeyama islands by the Kerama rift valley, and consequently formed two isolated island units. The Kuroshio warm current began to flow into the Okinawa trough from the Yonaguni Strait, and flow out through the Tsushima and Tokara straits also at 1.55 Ma, and these seaways effectively acted as barriers between the Ryukyu islands and Taiwan, China and Japan. Through this geological process, vicariant speciation generated Ryukyu endemic animal species. We support this hypothesis by drawing linearized maximum likelihood (ML) phylogenetic trees of the species in four endemic insect groups (peacock butterfly, Chinese windmill butterfly, golden‐ringed dragonfly, window firefly) using GenBank sequence data. We determined the precise branching ages for these phylogenetic trees, and show simultaneous speciation at 1.55 Ma for Amami–Okinawa and Yaeyama units. The Taiwan and Tsushima straits, barriers between Taiwan and China, and Japan and Korea, respectively, did not form sufficient barriers to migration during glacial low stands, and species were intermingled. A marine embayment may have posed as a migration barrier between northern and southern China in the Quaternary or a little earlier. From our study we also estimate the precise molecular evolution rate and justify the molecular clock.     

The impact of Quaternary climate oscillations on divergence times and historical population sizes in Thylamys opossums from the Andes

Climate oscillations during the Quaternary altered the distributions of terrestrial animals at a global scale. In mountainous regions, temperature fluctuations may have led to shifts in range size and population size as species tracked their shifting habitats upslope or downslope. This creates the potential for both allopatric speciation and population size fluctuations, as species are either constrained to smaller patches of habitat at higher elevations or able to expand into broader areas at higher latitudes. We considered the impact of climate oscillations on three pairs of marsupial species from the Andes (Thylamys opossums) by inferring divergence times and demographic changes. We compare four different divergence dating approaches, using anywhere from one to 26 loci. Each pair comprises a northern (tropical) lineage and a southern (subtropical to temperate) lineage. We predicted that divergences would have occurred during the last interglacial (LIG) period approximately 125 000 years ago and that population sizes for northern and southern lineages would either contract or expand, respectively. Our results suggest that all three north–south pairs diverged in the late Pleistocene during or slightly after the LIG. The three northern lineages showed no signs of population expansion, whereas two southern lineages exhibited dramatic, recent expansions. We attribute the difference in responses between tropical and subtropical lineages to the availability of ‘montane‐like’ habitats at lower elevations in regions at higher latitudes. We conclude that climate oscillations of the late Quaternary had a powerful impact on the evolutionary history of some of these species, both promoting speciation and leading to significant population size shifts.     

Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range.