Phylogeographic history of the yellow-necked fieldmouse (Apodemus flavicollis) in Europe and in the Near and Middle East

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of the Western Palearctic region are still needed. In this order, we sequenced 972 bp of the mitochondrial DNA cytochrome b (mtDNA cyt b) from 124 yellow-necked fieldmice (Apodemus flavicollis) collected from 53 European localities. The aims of the study were to answer the following questions: Did the Mediterranean peninsulas act as the main refuge for yellow-necked fieldmouse or did the species also survive in more easterly refugia (the Caucasus or the southern Ural) and in Central Europe? What is the role of Turkey and Near East regions as Quaternary glacial refuges for this species and as a source for postglacial recolonisers of the Western Palearctic region? The results provide a clear picture of the impact of the quaternary glaciations on the genetic and geographic structure of the fieldmouse. This species survived the ice ages in two main refuges, the first one in the Italo-Balkan region; the second one in Turkey and the Near East regions. It is from the Balkan refuge that it recolonised all European regions at the end of the last glaciation. The Turkish and Near East populations are distinct from the European ones and they did not recolonise the Palearctic region probably because: (i) they were blocked by the Black Sea and the Caucasus, (ii) the long term presence of fieldmice populations in the Balkans prevented their expansion. These are genetically differentiated from the European and Russian ones and could be described as a particular subspecies. This result emphasises the importance of Turkey and the Near and Middle East regions as a refuge for Palearctic mammals.     

Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation

Using the phylogeographic framework, we assessed the DNA sequence variation at the mitochondrial cytochrome b gene across the distribution range of the barbel Barbus barbus, a widely distributed European cyprinid. Reciprocal monophyly of non-Mediterranean European and Balkan/Anatolian populations is taken as evidence for a long-term barrier to gene flow, and interpreted as a consequence of survival of the species in two separate refugia during several later glacial cycles. Lack of profound genealogical divergence across Europe from western France to the northwestern Black Sea basin is consistent with recent colonization of this area from a single glacial refuge, which was probably located in the Danube River basin. This may have occurred in two steps: into the Western European river basins during the last interglacial, and throughout the Central European river basins after the last glacial. The populations from the Balkans and Anatolia apparently did not contribute mitochondrial DNA to the post-Pleistocene colonization of non-Mediterranean Europe. Lack of detectable variation within the Balkans/Anatolia is attributed mainly to recent expansion throughout these regions, facilitated by the freshwater conditions and seashore regression in the Black Sea during the Late Pleistocene and Early Holocene.     

Phylogeography and species limits in the green woodpecker complex (Aves: Picidae): multiple Pleistocene refugia and range expansion across Europe and the Near East

The green woodpecker complex consists of the green woodpecker (Picus viridis), distributed from Western Europe to the Caucasus and Iran, and the related LeVaillant's woodpecker (P. vaillantii), distributed in north‐western Africa from central Morocco to Tunisia. Much of the habitat of green woodpeckers in Central and Northern Europe was covered by ice, tundra, steppe or other unsuitable habitat during the Pleistocene; consequently, they must have come to occupy most of their current range during the past 20 000 years. We used complete mitochondrial ND2 sequences from populations throughout the range to investigate the genetic structure and evolutionary history of this complex. Three well‐differentiated clades, corresponding to three biogeographical regions, were recovered; 89% of the total genetic variance was distributed among these three regions. The populations in North Africa were sister to those of Europe and, within Europe, Iberia was sister to the rest of Europe and the Near East. This suggests that the post‐glacial colonization of most of Europe occurred from a refuge east of Iberia, probably in Italy or the Balkans; there was no substantial divergence among these regions. In addition, a population sample from Iran was genetically distinct from those of Western Europe, indicating a history of genetic isolation and an additional Pleistocene refuge east of the well‐known Balkan refugia and south of the Caucasus. Within Europe, northern populations were less genetically variable than southern ones, consistent with recent colonization. There was significant isolation‐by‐distance across Europe, indicating restricted gene flow; this was particularly apparent between western populations and those of the Caucasus and Iran. We recognize four species in the complex. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 710–723.     

Dispersal and colonisation, long and short chronologies: how continuous is the Early Pleistocene record for hominids outside East Africa?

This paper examines the evidence for hominids outside East Africa during the Early Pleistocene. Most attention has focused recently on the evidence for or against a late Pliocene dispersal, ca. 1.8 Ma., of hominids out of Africa into Asia and possibly southern Europe. Here, the focus is widened to include North Africa as well as southern Asia and Europe, as well as the evidence in these regions for hominids after their first putative appearance ca. 1.8 Ma. It suggests that overall there is very little evidence for hominids in most of these regions before the Middle Pleistocene. Consequently, it concludes that the colonising capabilities of Homo erectus may have been seriously over-rated, and that even if hominids did occupy parts of North Africa, southern Europe and southern Asia shortly after 2 Ma, there is little evidence of colonisation. Whilst further fieldwork will doubtless slowly fill many gaps in a poorly documented Lower Pleistocene hominid record, it appears premature to conclude that the appearance of hominids in North Africa, Europe and Asia was automatically followed by permanent settlement. Rather, current data are more consistent with the view that Lower Pleistocene hominid populations outside East Africa were often spatially and temporally discontinuous, that hominid expansion was strongly constrained by latitude, and that occupation of temperate latitudes north of latitude 40 degrees was largely confined to interglacial periods.     

Phylogeography and postglacial dispersion of the chub (Leuciscus cephalus) in Europe

A phylogeographic analysis of mitochondrial DNA variation was performed in order to test the hypothesis of a postglacial recolonization of mid- and north-European rivers from a Danubian refuge. Over 345 chub specimens from European rivers covering most of the species' native range were investigated using 600 bp of the cytochrome b gene. Chub in European rivers belong to four highly divergent mitochondrial groups (lineages) differing by mean divergence estimates from 5.2% to 7.89%. These four lineages have a largely allopatric distribution, implying four geographical sets: two Mediterranean, and two north-European sets. This pattern provided strong evidence for: (i) the eradication of this species from most of Europe during maximum ice extent; (ii) its survival in four refugia (Adriatic side of the Balkans, eastern Greece (Aegean Rivers), southern tributaries of the Danube, and periphery of Black and Caspian Seas); (iii) a differential postglacial recolonization of mid- and northern Europe from the last two refugia only; (iv) the occurrence of this recolonization in two steps for the Danubian (western) lineage that entered western Europe (Rhine-Rhone-Loire drainages) during the Riss-Würm interglacial period and survived the last glaciation there before colonizing Garonne, UK and German drainages up to the Elbe during the Holocene; and (v) the occurrence of this recolonization in a single step for the Ponto-Caspian (eastern) lineage that entered the Baltic area as far as the Oder in the Holocene. Both lineages came into contact in the River Elbe without evident mixing.     

Description of two new species of the genus Gobio (Teleostei: Cyprinidae) from the Black Sea coast of Turkey

Thesystematics of the genus Gobio, especially of the populations on the southern Black Sea coast, seems to be still far from being resolved. Seven species were rec-orded from the northern Black Sea coast while three species were recognized from the southern Black Sea coast. We examined in total 43 specimens from K?z?l?rmak River (southern Black Sea basin), 80 specimens from Çoruh River (the Western Cau-casus of the Black Sea basin), 14 specimens from Rioni River (the Western Caucasus of the Black Sea basin), and 6 specimens from Kherota and Shakhe Rivers (the Western Caucasus of the Black Sea basin). Based on an analysis of 32 metric and 5 meristic data as well as the number of vertebrae, we concluded that the K?z?l?rmak and Coruh populations are two distinct, unnamed species, and we describe them here as Gobio kizilirmakensis from the K?z?l?rmak River and G. artvinicus from the Çoruh River.

http://www.zoobank.org/urn:urn:lsid:zoobank.org:pub:1ED54FB1-588F-4412-B376-4BE4E4516EB1     

Low mitochondrial divergence indicates a rapid expansion across Europe in the weather loach, Misgurnus fossilis (L.)

Several phylogeographic studies using mtDNA sequence data have revealed an expressed geographic structure in nearly every European freshwater fish species studied. The authors present a phylogeographic study of Misgurnus fossilis on the base of 43 specimens from 17 localities across a major part of the known distribution area of M. fossilis . Despite the large geographic distance between the sampling points and their origin from different major European river systems, only eight closely related haplotypes in the sequences of the whole mitochondrial cytochrome b were detected. The most common haplotype I included more than 60% of specimens and occurred in the North Sea basin in northern Germany, in the Danube and Elbe basins in the Czech Republic, in the Nieman basin in Poland and in the Dniester and Vistula basins in the Ukraine. Since the highest number of haplotypes (six out of eight) and the most divergent haplotypes were found in the Danube, the authors tentatively consider the Danube to have acted as a refuge area for Misgurnus during the glaciation maxima in the Pleistocene. From this refuge, the species presumably recolonized Central and Eastern Europe but failed to stretch to Western Europe.     

Linnaeus' Neptunea (Mollusca: Gastropoda)

Three species of the arcto-boreal, large gastropod Neptunea , described by Linnaeus in 1758 and 1771, occur in large numbers over wide areas of the inshore North Atlantic and adjacent Arctic seas and are conspicuous among Pliocene and Pleistocene molluscs in the Icelandic, North Sea, and western Mediterranean basins. Selections of lectotypes for these species from shells in the collection of the Linnean Society of London, and designations of their type localities, establish the identity of Linnaeus' neptunes and more accurately determine their geographic and geologic distribution. The geographic range of Neptunea (Neptunea) antiqua (L.), the type species, now extends from southern Norway to the northern Biscay coast of France and from the westernmost Baltic Sea to southwestern Ireland; this species also occurs in Pliocene-Holocene marine deposits in West and East Germany, Sweden, the Netherlands, England and France. Its type locality is determined to be the North Sea. N. (Neptunea) despecta (L.) lives in the eastern Canadian Arctic, off southern Greenland, the Barents Sea, and North Atlantic as far south as Massachusetts and Portugal; it also occurs in Pliocene-Holocene strata of eastern Canada, east-central Greenland, Norway (including Svalbard), the Soviet Union, Sweden and England. Its type locality is determined to be the postglacial deposits at Uddevalla in southwestern Sweden. N. (Sulcosipho) contraria (L.) now extends from the southern Biscay coast of France to Cape Spartel, Morocco; this species also occurs in Pleistocene and lower Holocene sequences of the western Mediterranean. Its type locality is determined to be Vigo Bay, Spain. A closely related fossil species, N. (S.) angulata (S. V. Wood), occurs in Pliocene and Pleistocene deposits of the North Sea basin.     

Phylogeography of Scots pine in Europe and Asia based on mtDNA polymorphisms

We analyzed mitochondrial DNA polymorphisms to search for evidence of the genetic structure and patterns of admixture in 124 populations (N = 1407 trees) across the distribution of Scots pine in Europe and Asia. The markers revealed only a weak population structure in Central and Eastern Europe and suggested postglacial expansion to middle and northern latitudes from multiple sources. Major mitotype variants include the remnants of Scots pine at the north-western extreme of the distribution in the Scottish Highlands; two main variants (western and central European) that contributed to the contemporary populations in Norway and Sweden; the central-eastern European variant present in the Balkan region, Finland, and Russian Karelia; and a separate one common to most eastern European parts of Russia and western Siberia. We also observe signatures of a distinct refugium located in the northern parts of the Black Sea basin that contributed to the patterns of genetic variation observed in several populations in the Balkans, Ukraine, and western Russia. Some common haplotypes of putative ancient origin were shared among distant populations from Europe and Asia, including the most southern refugial stands that did not participate in postglacial recolonization of northern latitudes. The study indicates different genetic lineages of the species in Europe and provides a set of genetic markers for its finer-scale population history and divergence inference.     

Caucasus Mountains divide postulated postglacial colonization routes in the white‐breasted hedgehog,Erinaceus concolor

For many European species, the mountains of the Alps and the Pyrenees have acted as significant barriers to northwards colonization from southern glacial refugia. To the east, the Caucasus Mountains would seem to have been a similar barrier to the white‐breasted hedgehog (Erinaceus concolor). A deep divergence among hedgehog mitochondrial sequences to the north and south of the Caucasus Mountains suggests two colonization routes, originating from separate refugial regions and divided by this mountain barrier. From a Balkan refugium, hedgehogs have colonized northwards into Russia and to the northern foothills of the Caucasus Mountains. The origins of hedgehogs colonizing the southern parts of the Caucasus are not entirely clear, although fossil and climatic data suggest a glacial refugium on the southern shores of the Black Sea. Divergence within the southern group indicates a long‐standing fragmentation within such a refugium or the presence of further cryptic refugia in Turkey and the Near East. The Caucasus barrier would seem to have been an important factor in structuring the late Pleistocene distribution of species.     

Phylogeography and taxonomic status of trout and salmon from the Ponto‐Caspian drainages,with inferences on European Brown Trout evolution and taxonomy

Current taxonomy of western Eurasian trout leaves a number of questions open; it is not clear to what extent some species are distinct genetically and morphologically. The purpose of this paper was to explore phylogeography and species boundaries in freshwater and anadromous trout from the drainages of the Black and the Caspian Seas (Ponto‐Caspian). We studied morphology and mitochondrial phylogeny, combining samples from the western Caucasus within the potential range of five nominal species of trout that are thought to inhabit this region, and using the sequences available from GenBank. Our results suggest that the genetic diversity of trout in the Ponto‐Caspian region is best explained with the fragmentation of catchments. (1) All trout species from Ponto‐Caspian belong to the same mitochondrial clade, separated from the other trout since the Pleistocene; (2) the southeastern Black Sea area is the most likely place of diversification of this clade, which is closely related to the clades from Anatolia; (3) The species from the Black Sea and the Caspian Sea drainages are monophyletic; (4) except for the basal lineage of the Ponto‐Caspian clade, Salmo rizeensis, all the lineages produce anadromous forms; (5) genetic diversification within the Ponto‐Caspian clade is related to Pleistocene glacial waves; (6) the described morphological differences between the species are not fully diagnostic, and some earlier described differences depend on body size; the differences between freshwater and marine forms exceed those between the different lineages. We suggest a conservative taxonomic approach, using the names S. rizeensis and Salmo labrax for trout from the Black Sea basin and Salmo caspius and Salmo ciscaucasicus for the fish from the Caspian basin.     

Features of reproductive biology in females of bitterlings (Cyprinidae: Acheilognathinae) from the Amur River basin

Data on morphological and functional characteristics of the ovipositor, conical organ, and ovaries in four species of bitterlings (Russian bitterling Acanthorodeus asmussii, Khanka spiny bitterling A. chankaensis, bitterling Rhodeus sericeus, and Amur bitterling R. amurensis) from the Amur River basin are obtained and reviewed for the first time. In all studied fish species, several generations of sex cells develop at the same time, which leads to releasing of oocytes in batches. The specificity of Amur bitterling, bitterling, and Russian bitterling to selection of mollusks for egg deposition is determined.     

The Early Pliocene re-colonisation of the deep Mediterranean Sea by benthic foraminifera and their pulsed Late Pliocene–Middle Pleistocene decline

Ninety-five species and 19 genera of cosmopolitan, deep-sea benthic foraminifera belonging to the families Pleurostomellidae, Stilostomellidae and Nodosariidae, became extinct during the Late Pliocene–Middle Pleistocene. Only 50% of these (44 species) were present in the Pliocene or Pleistocene of the deep Mediterranean Sea (ODP Sites 654, 966, 967, 975, 976), being those which had successfully migrated in via the Strait of Gibraltar from the deep Atlantic following the annihilation of the Mediterranean deep-sea fauna during the Late Miocene Messinian Crisis. Most colonisation occurred within the first 0.8 myrs (5.3–4.5 Ma) after re-establishment of the Mediterranean–Atlantic link, with possibly a second lesser period of immigration in the Late Pliocene (3.4–3.0 Ma). We infer that colonisations may have been fortuitous and few in number, as some common members of the group in the Atlantic never succeeded in establishing in the Mediterranean Sea. There is no evidence of any new immigration events during the Pleistocene, implying that the present anti-estuarine circulation may have been in place throughout this period. Our studies suggest that these deep-water, low-oxygen-tolerant foraminifera survived the many periods of deep-water sapropel formation in the Pliocene–Early Pleistocene, possibly in somewhat shallower (~ 500 m) refuges with dysoxic, rather than anoxic conditions.The Pliocene–Pleistocene stratigraphic record of this group of elongate, cylindrical benthic foraminifera with constricted and specialised apertures is similar in the west and east Mediterranean basins. The group declined in abundance (flux) and diversity in two pulses, during the Late Pliocene (3.1–2.7 Ma) and the late Early Pleistocene (1.3–1.0 Ma) in concert with global, southern-sourced, deep-water sites (AABW, CPDW) and earlier than the single decline (1.0–0.6 Ma) in global, intermediate water sites (uNADW, AAIW). All species, with one possible exception, disappeared earlier in the Mediterranean than globally. The highest occurrence of any species of this group in Mediterranean sites was 0.8–0.43 Ma, comparable with 0.7–0.2 Ma outside with the youngest survivors being in abyssal, deep-water.Thus, despite the unusual oceanographic conditions and isolation, the deep Mediterranean Sea was in this case neither the centre for the evolution of new species nor a refuge where species survived after they had disappeared elsewhere.     

Exploring the Formation of a Disjunctive Pattern between Eastern Asia and North America Based on Fossil Evidence from Thuja (Cupressaceae)

Thuja, a genus of Cupressaceae comprising five extant species, presently occurs in both East Asia (3 species) and North America (2 species) and has a long fossil record from Paleocene to Pleistocene in the Northern Hemisphere. Two distinct hypotheses have been proposed to account for the origin and present distribution of this genus. Here we recognize and describe T. sutchuenensis Franch., a new fossil Thuja from the late Pliocene sediments of Zhangcun, Shanxi, North China, based on detailed comparisons with all living species and other fossil ones, integrate the global fossil records of this genus plotted in a set of paleomaps from different time intervals, which show that Thuja probably first appeared at high latitudes of North America in or before the Paleocene. This genus reached Greenland in the Paleocene, then arrived in eastern Asia in the Miocene via the land connection between East Asia and western North America. In the late Pliocene, it migrated into the interior of China. With the Quaternary cooling and drying, Thuja gradually retreated southwards to form today’s disjunctive distribution between East Asia and North America.     

Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

We sequenced 998 base pairs (bp) of mitochondrial DNA cytochrome b and 799 bp of nuclear gene BRCA1 in the Lesser white-toothed shrew (Crocidura suaveolens group) over its geographic range from Portugal to Japan. The aims of the study were to identify the main clades within the group and respective refugia resulting from Pleistocene glaciations. Analyses revealed the Asian lesser white-toothed shrew (C. shantungensis) as the basal clade, followed by a major branch of C. suaveolens, subdivided sensu stricto into six clades, which split-up in the Upper Pliocene and Lower Pleistocene (1.9-0.9 Myr). The largest clade, occurring over a huge range from east Europe to Mongolia, shows evidence of population expansion after a bottleneck. West European clades originated from Iberian and Italo-Balkanic refugia. In the Near East, three clades evolved in an apparent hotspot of refugia (west Turkey, south-west and south-east of the Caucasus). Most clades include specimens of different morphotypes and the validity of many taxa in the C. suaveolens group has to be re-evaluated.     

On the systematics and phylogeography of eight-barbel loaches of the genus Lefua (Cobitoidea: Nemacheilidae): mtDNA typing of L. pleskei

Comparative analysis of own sequence data for the mtDNA control region (926 to 928 bp) from eight-barbel loaches inhabiting eight localities in the Amur River basin (4) and the Sea of Japan (4) and the GeneBank/NCBI data for the Lefua individuals from the other regions of East Asia showed that eight-barbel loaches from Primorskii krai water basins were marked by a specific group of mtDNA haplotypes. This finding is considered as supporting the species status of L. pleskei. Genetic distances within L. pleskei are small (on average 0.35%) and close to those within L. nikkonis (on average 0.48%). The distances between this species pair are the least (on average 2.15%) among all other pairs compared. In MP, ML, and Bayesian trees, L. pleskei and L. nikkonis haplotypes formed a common clade with high statistically significant support. In all tree variants, L. costata mtDNA haplotypes were located out of the group of interest. A clade consisting of highly diverged lineages of Lefua sp. and L. echigonia haplotypes occupied a basal position. The mtDNA haplotypes of L. pleskei and L. costata from the Amur River basin were evolutionary young and derived from the haplotypes found in these species from the Sea of Japan (L. pleskei) or the Yellow Sea (L. costata) basins. It is thereby suggested that both species rather recently migrated into the Amur River system. According to the molecular clock data, basal diversification of the eight-barbel loach lineages took place at the end of middle Miocene (about 11 to 12 Myr ago), while divergence of L. pleskei and L. nikkonis ancestral forms probably occurred approximately, 5 Myr ago. Since all main lineages of eight-barbel loaches were found in the Sea of Japan basin (continental coastline and the islands), the divergence order and dispersal patterns of the Lefua species might have been largely determined by the geological development pattern of this water body and the adjacent territories.     

Phylogeography of noble crayfish (Astacus astacus) reveals multiple refugia

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Vicariance, colonisation, and fast local speciation in Asia Minor and the Balkans as revealed from the phylogeny of spined loaches (Osteichthyes; Cobitidae)

We reconstruct the phylogeny of the morphologically diagnosable subgenera Bicanestrinia, Beysehiria, and Cobitis sensu stricto of the genus Cobitis from Asia Minor and the Balkans. We used the complete cytochrome b gene of 65 specimens in order to infer their evolutionary history in this zoogeographically interesting area. Our phylogeographic analysis did not evidence the previously suggested monophyly of the Bicanestrinia subgenus but revealed five monophyletic lineages in the area: the lineages Bicanestrinia I-IV including all species of Bicanestrinia plus the lineage Cobitis s. str. The monotypic subgenus Beysehiria from Lake Beysehir in Anatolia was closely related to the syntopic population of C. turcica and nested inside the lineage Bicanestrinia III. The strictly allopatric distribution of the four lineages of Bicanestrinia suggests that vicariance has played a major role in the diversification of Bicanestrinia. All analysed species of Cobitis s. str. from Asia Minor and Balkans were closely related to Cobitis s. str. from Central Europe, the Danube basin and the Caucasus, indicating at least two colonisation events into Asia Minor and the Balkans. A third, recent colonisation event led to the presence of C. strumicae, generally restricted to the Aegean Sea drainage, in the Danube basin. Besides the evidences of vicariance and colonisation events in the phylogenetic history of the genus Cobitis in Asia Minor and the Balkans, our analysis suggested also a rapid morphological evolution of C. bilseli in a lacustrine environment. Application of Cobitis mitochondrial cytochrome b clocks of 0.68% sequence divergence per million years (MY) suggest that the split between the five major lineages happened approximately 12.4-17.6 MYA, and according to the lack of basal resolution of this monophyletic group probably the split of all lineages happened within a narrow time window.     

Tracing recent invasions of the Ponto-Caspian mysid shrimp Hemimysis anomala across Europe and to North America with mitochondrial DNA

The mysid crustacean Hemimysis anomala ('bloody-red shrimp') is one of the most recent participants in the invasion of European inland waters by Ponto-Caspian species. Recently the species also became established in England and the Laurentian Great Lakes of North America. Using information from mitochondrial cytochrome oxidase I (COI) gene sequences, we traced the invasion pathways of H. anomala ; the inferences were enabled by the observed phylogeographical subdivision among the source area populations in the estuaries of the Ponto-Caspian basin. The data distinguish two routes to northern and western Europe used by distinct lineages. One route has been to and through the Baltic Sea and further to the Rhine delta, probably from a population intentionally introduced to a Lithuanian water reservoir from the lower Dnieper River (NW Black Sea area) in 1960. The other lineage is derived from the Danube delta and has spread across the continent up the Danube River and further through the Main–Danube canal down to the Rhine River delta. Only the Danube lineage was found in England and in North America. The two lineages appear to have met secondarily and are now found intermixed at several sites in NW Europe, including the Rhine and waters linked with the man-made Mittellandkanal that interconnects the Rhine and Baltic drainage systems.     

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA,with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus

The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55–0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.