Refugia and phylogeography of Taiwania in East Asia

Aim The East Asia endemic Taiwania cryptomerioides Hayata is an iconic and relictual monotypic conifer whose main extant populations are now restricted to the Yunnan–Myanmar border, northern Vietnam and Taiwan. It has also been reported from several localities in Guizhou, Hubei and Fujian Provinces, China. Its fossil record indicates that, while it was more widely distributed in the Northern Hemisphere and grew under a range of different ecological conditions, it has remained almost unchanged in its morphology for over 100 Myr. We investigate whether these remaining extant, disjunct populations have diverged genetically; when such a divergence may have occurred; and which, if any, of the extant populations exhibit refugial characteristics. Location East Asia. Methods Sequences of five chloroplast DNA markers (petG–trnP, trnH–psbA, trnV–trnM, trnC–ycf6 and trnL–trnF) from all extant populations of T. cryptomerioides were analysed to reveal their phylogeography. Molecular clock models with fossil calibrations were used to estimate divergence times between extant populations. Results Extremely low nucleotide diversity was found in the overall population (π = 0.00077) with only nine haplotypes distinguished. The mainland Asia populations share one major ancestral haplotype. The insular populations in Taiwan all possess a unique haplotype with at least an eight‐mutational‐step difference to the mainland Asia haplotype. Molecular clock estimations demonstrated that the mean divergence time between the predominant insular population haplotype and the mainland Asia haplotype occurred at c. 3.23–3.41 Ma, followed by a split into Vietnamese and Yunnan–Myanmar populations (c. 1.0–1.39 Ma). Main conclusions Strong genetic differentiation exists between insular (Taiwan) and mainland Asia populations. The split between insular and mainland haplotypes can be dated back to the end of the Pliocene. The Yunnan–Myanmar border area, northern Vietnam and Taiwan are identified here as potential refugia for T. cryptomerioides. Other populations in mainland China are unlikely to be the result of historical fragmentation and their origins require further investigation.     

Biogeographical consequences of Cenozoic tectonic events within East Asian margins: a case study of Hynobius biogeography

Few studies have explored the role of Cenozoic tectonic evolution in shaping patterns and processes of extant animal distributions within East Asian margins. We select Hynobius salamanders (Amphibia: Hynobiidae) as a model to examine biogeographical consequences of Cenozoic tectonic events within East Asian margins. First, we use GenBank molecular data to reconstruct phylogenetic interrelationships of Hynobius by bayesian and maximum likelihood analyses. Second, we estimate the divergence time using the bayesian relaxed clock approach and infer dispersal/vicariance histories under the 'dispersal-extinction-cladogenesis' model. Finally, we test whether evolutionary history and biogeographical processes of Hynobius should coincide with the predictions of two major hypotheses (the 'vicariance'/'out of southwestern Japan' hypothesis). The resulting phylogeny confirmed Hynobius as a monophyletic group, which could be divided into nine major clades associated with six geographical areas. Our results show that: (1) the most recent common ancestor of Hynobius was distributed in southwestern Japan and Hokkaido Island, (2) a sister taxon relationship between Hynobius retardatus and all remaining species was the results of a vicariance event between Hokkaido Island and southwestern Japan in the Middle Eocene, (3) ancestral Hynobius in southwestern Japan dispersed into the Taiwan Island, central China, 'Korean Peninsula and northeastern China' as well as northeastern Honshu during the Late Eocene-Late Miocene. Our findings suggest that Cenozoic tectonic evolution plays an important role in shaping disjunctive distributions of extant Hynobius within East Asian margins.     

Phylogeography of the Japanese pipistrelle bat,Pipistrellus abramus,in China: the impact of ancient and recent events on population genetic structure

The influence of Pleistocene climatic oscillations on shaping the genetic structure of Asian biota is poorly known. The Japanese pipistrelle bat occurs over a wide range in eastern Asia, from Siberia to Japan. To test the relative impact of ancient and more recent events on genetic structure in this species, we combined mitochondrial (cytochrome b) and microsatellite markers to reconstruct its phylogeographic and demographic history on continental China and its offshore islands, Hainan Island and the Zhoushan Archipelago. Our mitochondrial DNA tree recovered two divergent geographical clades, indicating multiple glacial refugia in the region. The first clade was mainly confined to Hainan Island, indicating that gene flow between this population and the continent has been restricted, despite being repeatedly connected to the mainland during repeated glacial episodes. By contrast, haplotypes sampled on the Zhoushan Archipelago were mixed with those from the mainland, suggesting a recent shared history of expansion. Although microsatellite allele frequencies showed clear discontinuities across the sampling range, supporting the current isolation of both Hainan Island and the Zhoushan Archipelago, we also found clear evidence of more recent back colonization, probably via post‐glacial expansion or, in the latter case, occasional long distance dispersal. The results obtained highlight the importance of using multiple sets of markers for teasing apart the roles of ancient and more recent events on population genetic structure. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 582–594.     

Phylogeography and the origins of range disjunctions in a north temperate fish,the pygmy whitefish (Prosopium coulterii), inferred from mitochondrial and nuclear DNA sequence analysis

Aim To investigate the degree of phylogeographical divergence within pygmy whitefish (Prosopium coulterii) and to test hypotheses concerning the origin of disjunct populations within North America. Location North America from western Alaska to Lake Superior. Methods Mitochondrial (ATPase subunit VI) and nuclear (ITS‐1, ITS‐2) DNA sequence variation was assessed across the species’ North American range to test for the existence of distinct phylogeographical groupings of pygmy whitefish associated with known glacial refugia. Coalescent simulations of the mitochondrial DNA (mtDNA) data were used to test hypotheses of population structure. Results This species is composed of two monophyletic mitochondrial clades across its North American range. The two mtDNA clades differed by an average 3.3% nucleotide sequence divergence. These clades were also distinguished by ITS‐2, but the relationships among lineages were not resolved by the ITS‐1 analysis. Coalescent analyses rejected the null hypothesis of the current disjunct distributions being a result of fragmentation of a single widespread ancestral lineage across a variety of effective population sizes and divergence times. Main conclusions The current range disjunctions of pygmy whitefish in North America probably resulted from isolation, genetic divergence, and selective dispersal from at least two major Pleistocene glacial refugia: Beringia and Cascadia. More recent isolation and dispersal from an upper Mississippi refugium is suggested by relationships within one of the clades and by distributional evidence from co‐distributed species. The Beringian and Cascadian refugia have played major roles in the zoogeography of Nearctic temperate aquatics, but the roles of smaller refugia appear more variable among other species.     

Phylogeography of the genus Cardiandra based on genetic variation in cpDNA sequences

We investigated the phylogenetic relationships within the genus Cardiandra based on plastid DNA sequences. The phylogenetic tree showed that Cardiandra populations from the Ryukyu Islands (Japan) and Taiwan were monophyletic (Ryukyu–Taiwan clade), whereas taxa from China and mainland Japan were sisters to this clade. The divergence time between the Ryukyu–Taiwan clade and the other species was estimated to be 0.082 MYA, i.e., the late Pleistocene. The infrageneric and/or infraspecific differentiation of Cardiandra is estimated to have depended largely on allopatric differentiation caused by the presence or division of the past landbridge of the Ryukyu Islands, which connected mainland Japan to the Asian Continent during the Quaternary.     

Quaternary palaeoenvironmental oscillations drove the evolution of the Eurasian Carassius auratus complex (Cypriniformes,Cyprinidae)

Aim We sought to reconstruct the spatio‐temporal genetic diversification in goldfish of the Carassius auratus complex, which is widely distributed in Eurasia, to test whether vicariance events or human‐mediated translocations best explained lineage divergence and genogeographical history. Location East Asia and the Oriental islands including Japan, the Ryukyus and Taiwan, and Europe, including Russia and the Czech Republic. Methods We reconstructed the matrilineal history of Eurasian goldfish using 1876 sequences from the partial mitochondrial DNA control region (426 bp) and 191 complete sequences of cytochrome b (1140 bp) from 67 localities representing most of the range of the species. Divergence times were estimated using a Bayesian Markov chain Monte Carlo approach based either on molecular clock data or on the fossil record. Genetic structure and the historical demography of populations were analysed using partial correlation tests and analyses of molecular variance. Results Three lineages had high levels of regional specificity. Lineages A and B from the main islands of Japan differed greatly from lineage C, which occurred on the mainland, Taiwan and the Ryukyus. Lineages A and B had late Pliocene origins. Six geographically constrained sublineages within lineage C had near‐simultaneous mid‐Pleistocene divergences. Main conclusions Genetic structure in the C. auratus complex appears to have been driven by palaeoenvironmental perturbations rather than human translocations. The disappearance of a land bridge in the Tsushima Strait around 3.0 Ma is responsible for the separation of Japanese and continental lineages; the estimated divergence time is 2.75–2.32 Ma. Fujian, China and Vietnam appear to have provided important refugia for the C. auratus complex during glaciation. After warm, moist summer monsoons intensified during the mid‐Pleistocene, goldfish are likely to have dispersed north‐eastwards to recolonize the Ryukyus via Taiwan and northwards to recolonize mainland China.     

Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan

Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.     

Ecological and geological processes impacting speciation modes drive the formation of wide-range disjunctions within tribe Putorieae (Rubiaceae)

Wide-range geographically discontinuous distributions have long intrigued scientists. We explore the role of ecology, geology, and dispersal in the formation of these large-scale disjunctions, using the angiosperm tribe Putorieae (Rubiaceae) as a case study. From DNA sequences of nuclear ITS and six plastid markers, we inferred a phylogeny with 65% of all known Putorieae species. Divergence times, ancestral ranges, and diversification rate shifts were then estimated using Bayesian inference. We further explored species climatic tolerances and performed ancestral niche reconstruction to discriminate among alternative speciation modes, including geographical and ecological vicariance, and ecogeographical, ecological, and dispersal-mediated speciation. As a result, we identified seven major clades in Putorieae, some of which exhibit striking geographical disjunctions, matching the Rand Flora pattern, with sister species in the Canary Islands andeastern and southern Africa. Initial diversification within the tribe occurred in the early Miocene, coincident with a period of climate warming; however, most clades diverged within the last 10 Myr. Aridification and high extinction rates, coupled with ecological vicariance, explain the oldest disjunctions. Adaptation to new environmental conditions, after allopatry, is observed in several clades. Dispersal, either long-distance or via corridors made available by mountain uplift, is behind the most recent disjunctions. Some of these events were followed by ecological speciation and rapid diversification, with species becoming adapted to xeric or increasingly colder continental climates. We show that an integrative approach may help discriminate among speciation modes invoked to explain disjunctions at macroevolutionary time scales, even when extinction has erased the signature of past events.     

Phylogeography of a Patagonian lizard and frog: Congruent signature of southern glacial refuges

Pleistocene glaciations produced significant increases in continental ice cover in polar and mid‐latitude temperate areas, sea‐level declines and shifts and reshuffling of biomes, all of which promote either isolation, coalescence or fragmentation in the distribution of land biota. If populations of several taxa have been co‐distributed for a prolonged time, and if the periods between perturbation or vicariance processes have been more or less stable, it is expected that divergence patterns of closely related and ecologically similar species will be congruent because of their similar biological and demographic characteristics. Based on this premise, we analysed the phylogeographic structure (cytochrome b) of Liolaemus pictus and Batrachyla leptopus, two widely co‐distributed lizard and frog species, respectively, in the Chiloé Archipelago of southern Chile, to decipher their genetic structure in response to a common climatic and environmental history. Haplotype network analysis and Bayesian inference suggest an evolutionary pattern of genetic diversity for the two species that is consistent with the Quaternary glacial history of southern Chile, and suggests a complex phylogeographic history in the Liolaemus and Batrachyla species. High‐divergence levels among haplotypes in some island populations of the archipelago also suggest genetic connectivity between putative refuges from Chiloé Island and the mainland along the exposed continental shelf during sea level minima associated with the most recent Quaternary glaciations. Our results are consistent with our hypothesis that two species have responded to parallel historical events in which the historical process during the last glacial maximum (approximately 41°S) has been sufficient to influence their phylogeographic structure.     

Multiple origins of Locusta migratoria (Orthoptera: Acrididae) in the Japanese Archipelago and the presence of two major clades in the world: evidence from a molecular approach

Phylogenetic relationships among migratory locust (Locusta migratoria) populations in different climatic regions were analysed by sequencing four mitochondrial DNA regions, with special reference to the origin of Japanese populations. The populations are clearly separated into two clades: one consists of individuals from temperate and cold‐temperate areas of Japan and the Chinese continent, and the other comprises those from subtropical islands of Japan, Hainan Island in China, Timol Leste, Australia, Ethiopia, France, and some individuals from Tsushima Island and Honshu of Japan. The divergence time between the two clades is estimated to be 0.86–1.89 Mya. The phylogenetic analysis revealed that Japanese L. migratoria populations were composed of individuals of six different origins: (1) Hokkaido populations possibly from the Russian continent; (2) Honshu–Kyushu populations from the Chinese continent; (3) Southwest Island populations from Hainan Island or adjacent areas; (4) Ogasawara populations that might have originated from Micronesia; (5) part of the Tsushima population that originated from somewhere in the Asian tropics; and (6) a possible relict population of ancient southern haplotypes that exists in western areas of northern Honshu. The Tsugaru Straits and Tokara Straits have acted as effective geographical barriers, as in other organisms, isolating locust populations for a few thousand years. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 570–581.     

Glacial Effects on Sequence Divergence of Mitochondrial COII of Polyura eudamippus (Lepidoptera: Nymphalidae) in China

Sequence divergence of mitochondrial COII was analyzed in 50 specimens belonging to five subspecies of Polyura eudamippus (Lepidoptera: Nymphalidae) collected from southern China. There were nine haplotypes in the 405 bp of partial COII sequence. Distribution of the five subspecies was primarily consistent with the spatial distribution of haplotypes. The K _st statistic showed genetic differentiation among these subspecies, except between the pair of P. e. kuangtungensis and P. e. formosana, which were separated by the Taiwan Strait. This is consistent with the 10,000-year history of the Taiwan Strait, not long enough for detectable differentiation. The present distribution pattern of COII haplotypes of P. eudamippus should be shaped by the alteration of Pleistocene glaciations, and Yunnan might be the refugium of P. eudamippus in the ice age, judging from the abundant haplotypes remaining. There were two routes for P. eudamippus in the postglacial expansion, one northward to Sichuan, Chongqing, and Hubei and another eastward to the southeastern coast of mainland China and Taiwan Island. Because the haplotype of butterflies on Hainan Island (P. e. whiteheadi) was completely different from that of mainland China, it was estimated that butterflies on Hainan Island might be from the Indo-China Peninsula rather than from mainland China.     

Phylogenetic,Demographic and Dating Analyses of Bufo gargarizans Populations from the Zhoushan Archipelago and Mainland China

Relatively little is known about the relationship between Bufo gargarizans populations from Zhoushan Archipelago and nearby continental regions on the Pacific coast of eastern China.In this paper,155 new specimens of B.gargarizans from Zhoushan Archipelago and adjacent continents and 71 published specimens of B.gargarizans from mainland China were studied.Phylogeographical and dating analyses of B.gargarizans were performed using mitochondrial DNA sequencing with a length of 1436 bp.A mt DNA tree that indicated seven major clades was obtained.The earliest split in the mt DNA tree corresponding to the divergence of populations from the western highland region occurred approximately 4.0 million years ago(mya).A subsequent clade occurred about 3.4 mya,with cladogenesis continuing toward the end of the Pleistocene.The continental clades were distributed in the western,central and northeastern regions of China.Zhoushan Archipelago clades consisted of two largely geographically overlapping subclades with the mt DNA divergence time of 0.73 mya.These results indicated there was extensive dispersal after vicariance.The B.gargarizans populations on Zhoushan Archipelago most probably originated from populations in nearby eastern continental regions of China.It was concluded that geological uplifting during the Pliocene and several sea-level changes in Pleistocene might have influenced the divergence and population demographical history of this species.     

MOLECULAR AND GEOLOGIC EVIDENCE OF SHARED HISTORY BETWEEN HERMIT CRABS AND THE SYMBIOTIC GENUS HYDRACTINIA

The paleobiogeographic histories of three North Atlantic hermit crab lineages were compared with a single-copy DNA-DNA hybridization phylogeny of their symbiotic hydroid genus Hydractinia to test hypotheses of shared history between these host and symbiont lineages. A survey of the geologic literature suggests that two vicariance events in the Quaternary are responsible for existing range disjunctions of the host hermit crab lineages. The Hydractinia phylogeny revealed two distinct clades, one with a primarily northern and the other with a primarily southern distribution. In two of three cases, hydroids associated with closely related hermits on both sides of the range disjunction appear as sister taxa in the phylogeny. A linear scaling between a measure of hydroid sequence divergence and independent geologic estimates of the timing of the vicariant events believed to have established the hermit crab range disjunctions is consistent with the claim of temporal coincidence of cladogenic and vicariance events. These findings provide evidence for shared history of symbiotic associations in two of the three cases.     

Genetic evidence for the origins of range disjunctions in the Australian dry sclerophyll plant Hardenbergia violacea

Aim The distribution of genetic variation in the Australian dry sclerophyll plant Hardenbergia violacea (Fabaceae) is examined in the context of Pleistocene climate change in order to identify likely refugia. Particular consideration is given to the origin of range disjunctions in South Australia and Tasmania, and to determining whether the Tasmanian population is indigenous or recently introduced from mainland Australia. Location Southeastern Australian mainland and Tasmania. Methods A combination of chloroplast polymerase chain reaction–restriction fragment length polymorphism and genomic amplified fragment length polymorphism (AFLP) marker systems was used to examine the genetic structure of 292 individuals from 13 populations across the range of H. violacea in southeastern Australia. Results Hardenbergia violacea populations in Tasmania and southern Victoria were characterized by low, almost monotypic chloroplast diversity. New South Wales showed higher haplotype diversity and haplotype sharing among widely distributed populations. Principal coordinates analysis (PCoA) of the AFLP data found a strong latitudinal cline in AFLP variation from northern New South Wales south to Tasmania. The Tasmanian population formed an isolated and somewhat disjunct genetic cluster at one end of this cline. However, the South Australian population was an exception to the clinal variation shown by all other populations, forming a highly disjunct cluster in the PCoA. Within‐population genetic diversity was low in both disjunct populations. Main conclusions The genetic evidence indicates that the Tasmanian population is likely to be indigenous and probably the product of vicariance, which was followed by range contraction at the Last Glacial Maximum or an earlier glacial event. The deep phylogenetic disjunction in South Australia is evidence of a much earlier separation on mainland Australia. The chloroplast structure indicates that, during the Pleistocene, H. violacea underwent broad‐scale recolonization in southern Victoria and Tasmania, possibly from a large continental refugium in eastern New South Wales. We conclude that H. violacea, and presumably the sclerophyll communities in which it occurs, have undergone multiple range contractions to large continental refugia during different Pleistocene glaciations in southeastern Australia.     

Mitochondrial DNA Sequence-Based Population Genetic Structure of the Firefly, Pyrocoelia rufa (Coleoptera: Lampyridae)

The genetic divergence, population genetic structure, and possible speciation of the Korean firefly, Pyrocoelia rufa, were investigated on the midsouthern Korean mainland, coastal islets, a remote offshore island, Jedu-do, and Tsushima Island in Japan. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 20 mtDNA-sequence-based haplotypes with a maximum divergence of 5.5%. Phylogenetic analyses using PAUP, PHYLIP, and networks subdivided the P. rufa into two clades (termed clade A and B) and the minimum nucleotide divergence between them was 3.7%. Clade A occurred throughout the Korean mainland and the coastal islets and Tsushima Island in Japan, whereas clade B was exclusively found on Jeju-do Island. In the analysis of the population genetic structure, clade B formed an independent phylogeographic group, but clade A was further subdivided into three groups: two covering western and eastern parts of the Korean peninsula, respectively, and the other occupying one eastern coastal islet and Japanese Tsushima Island. Considering both phylogeny and population structure of P. rufa, the Jeju-do Island population is obviously differentiated from other P. rufa populations, but the Tsushima Island population was a subset of the Korean coastal islet, Geoje. We interpreted the isolation of the Jeju-do population and the grouping of Tsushima Island with Korean coastal islets in terms of Late Pleistocene-Holocene events. The eastern-western subdivision on the Korean mainland was interpreted partially by the presence of a large major mountain range, which bisects the midpart of the Korean peninsula into western and eastern parts.     

Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of Taiwan.

In this study, we investigated the genetic structure and phylogeographic pattern of the genus Cunninghamia, a member of the Cupressaceae restricted to mainland China and Taiwan, based on sequences of the trnD-trnT noncoding spacer of the chloroplast DNA. Maternal inheritance of chloroplasts was determined experimentally. No paternal leakage was detected. Both parsimony and neighbor-joining analyses revealed the polyphyly of Cunninghamia konishii, populations of which were nested in clades of C. lanceolata from mainland China. The nucleotide diversity of chloroplast DNA sequences within C. konishii (0.0118) was higher than that between species (0.0104), which agrees with a previous allozyme investigation. Based on mutational differences between sequences, a minimum spanning network consisting of five clades was constructed. Significant genetic differentiation (phiST = 0.130, P < 0.001) was detected between the clades based on AMOVA analyses. We infer several possible refugia in the Yunnan, Zhejiang, and Guangdong provinces of south China, all located in the minimum network as interior nodes. We also infer possible migration routes of Cunninghamia populations. The phylogeographic pattern shown in the reconstructed network suggests that the present-day Cunninghamia populations in Taiwan were derived from six different sources in continental Asia via long-distance seed dispersal. A migrant-pool model explains the heterogeneous composition of the organelle DNA in Taiwan's populations and the low differentiation between populations of Taiwan and China (phiCT = 0.012, P = 0.454). In contrast with the genetic heterogeneity within geographic populations, many local populations have attained coalescence at the trnD-trnT alleles, which has led to significant differentiation at the population level.     

Phylogeography of the fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), in Taiwan

A phylogenetic analysis of Taiwanese fanged dicroglossine frog, Limnonectes fujianensis (Anura, Ranidae), was conducted to examine its genetic diversification using sequence data from a portion of the mitochondrial DNA (mtDNA) cytochrome b sequences. We collected genetic data from 200 individuals at 23 localities in Taiwan and three localities in China. A neighbor-joining tree of 39 haplotypes revealed two clades in Taiwan and a clade in China, each showing restricted geographical distribution. The pattern of geographical divergence suggests a single invasion into Taiwan. Divergence times between clades were inferred using molecular clock tests. The population relationship of L. fujianensis between Taiwan and mainland China, and the phylogenetic relationships with its congeners, e.g., L. bannaensis, L. fragilis and L. kuhlii, were obtained and discussed.     

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.