Mitochondrial DNA data imply a stepping‐stone colonization of Beringia by arctic warbler Phylloscopus borealis

Arctic warbler Phylloscopus borealis is one of several high‐latitude Passerines which are widely distributed across one northern continent but restricted to the Beringian part of the other. Most species with such asymmetric intercontinental ranges are monomorphic across Beringia, suggesting either recent colonization of the second continent or considerable gene flow across the Bering Strait. Arctic warbler is the only migratory species in this group that has three different subspecies in Beringia: Ph. b. borealis (Scandinavia to western Beringia, south to Mongolia), Ph. b. xanthodryas (Japan, Sakhalin, Kamchatka, western Beringia), and Ph. b. kennicotti (Alaska). This polymorphism may indicate that Arctic warbler has a unique and complex phylogeographic history that differs significantly from other species with similar ranges. Our analyses of complete mtDNA ND2 sequences of 88 Arctic warblers collected across the species range showed that the clade comprised of birds breeding on Sakhalin Island and Kamchatka Peninsula diverged from the Palearctic/Beringian clade by 3.8% in ND2 sequence. Beringian birds formed a recently derived clade embedded within the Palearctic clade. Nucleotide diversity declined sharply eastward from Palearctic to western Beringia and then to eastern Beringia. Our data provided no support for currently recognized subspecies. They suggested that the barrier at the western edge of Beringia was crossed by Arctic warbler earlier than the Bering Strait resulting in a stepping‐stone colonization of Beringia by this species. Gene flow appears to be restricted across the western border of Beringia but not the Bering Strait.     

Old divergences in a boreal bird supports long-term survival through the Ice Ages

Background  

Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species.     

A spatial aspect on mitochondrial DNA genealogy in Apodemus peninsulae from East Asia

Apodemus peninsulae is a field mouse that inhabits the broad-leafed forests of temperate Eurasia. We examined the mitochondrial cytochrome b gene in 57 individuals of A. peninsulae from northeastern Asia, including Siberia, Primorye, Magadan region, Sakhalin, Hokkaido, and the Korean Peninsula. The genealogy of the mitochondrial DNA (mtDNA) in A. peninsulae was shown to have substantial geographic affinity, suggesting geographic architecture of northeastern Asia, including the islands of Sakhalin and Hokkaido, played important roles on the cladogenesis. Taking into account the presence of region-specific anciently divergent mtDNA types, three parts of the regions of Primorye, Siberia, and the Korean Peninsula can be denoted as refugia for A. peninsulae during the substantial period of the Quaternary glacial ages. Among the geographic regions examined, Primorye is likely to be the most influential one, from which the mtDNA is thought to have migrated to the neighboring regions of Sakhalin, Hokkaido, the Magadan region, and Siberia during the evolution of this species.     

Taxonomy and Distribution of Freshwater Pearl Mussels (Unionoida: Margaritiferidae) of the Russian Far East

The freshwater pearl mussel family Margaritiferidae includes 13 extant species, which are all listed by IUCN as endangered or vulnerable taxa. In this study, an extensive spatial sampling of Margaritifera spp. across the Russian Far East (Amur Basin, Kamchatka Peninsula, Kurile Archipelago and Sakhalin Island) was conducted for a revision of their taxonomy and distribution ranges. Based on their DNA sequences, shell and soft tissue morphology, three valid species were identified: Margaritifera dahurica (Middendorff, 1850), M. laevis (Haas, 1910) and M. middendorffi (Rosén, 1926). M. dahurica ranges across the Amur basin and some of the nearest river systems. M. laevis is distributed in Japan, Sakhalin Island and the Kurile Archipelago. M. middendorffi was previously considered an endemic species of the Kamchatka. However, it is widespread in the rivers of Kamchatka, Sakhalin Island, the Kurile Islands (across the Bussol Strait, which is the most significant biogeographical boundary within the archipelago), and, likely, in Japan. The Japanese species M. togakushiensis Kondo & Kobayashi, 2005 seems to be conspecific with M. middendorffi because of similar morphological patterns, small shell size (<100 mm long) and overlapped ranges, but it is in need of a separate revision. Phylogenetic analysis reveals that two NW Pacific margaritiferid species, M. laevis and M. middendorffi, formed a monophyletic 18S rDNA clade together with the North American species M. marrianae and M. falcata. The patterns that were found in these Margaritifera spp. are similar to those of freshwater fishes, indicating multiple colonizations of Eastern Asia by different mitochondrial lineages, including an ancient Beringian exchange between freshwater faunas across the Pacific.     

Mitochondrial DNA haplogrouping of the brown bear,Ursus arctos (Carnivora: Ursidae) in Asia,based on a newly developed APLP analysis

Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA‐haplogrouping U. arctos specimens by detecting haplogroup‐specific SNPs. We verified the validity and utility of this method by analysing up to 170‐year‐old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 627–635.     

Phylogeographic patterns in the great spotted woodpecker Dendrocopos major across Eurasia

We sequenced parts of three mitochondrial genes in 67 great spotted woodpeckers Dendrocopos major taken from 17 sites across Eurasia and Japan. Two groups, differing by ca. 3% sequence divergence, were determined to have had independent evolutionary histories: samples from the southeast (Sakhalin, Primor'e, Hokkaido), and the rest of Eurasia. The southeastern group corresponds to the subspecies D. m. japonicus , which will likely merit species status upon study of all subspecies; at present it should be considered an evolutionarily significant unit. From the United Kingdom to the Russian North Pacific, no phylogeographic divisions were found, which is likely a result of recent range expansion following retreat of permafrost after the last ice age.     

Mitochondrial DNA variation pattern in larches of Eastern Siberia and the Far East

Genetic variation has been studied in 32 Eastern Siberian and Far Eastern populations of Larix Mill. with the use of three mitochondrial markers based on polymerase chain reaction. Eight multilocus haplotypes with a heterogeneous spatial distribution (G _ST = 0.788, N _ST = 0.829) have been found, which indicates limited gene flows between populations. Several geographic regions with specific larch haplotype sets have been determined: (1) Japan, (2) southern Sakhalin and the Kuril Islands, (3) Primor’e and Korea, (4) Kamchatka, and (5) Eastern Siberia and the northern Far East. The haplotype fixed in the Kamchatka is absent in the Magadan oblast or Chukotka but is present in southern Primor’e and Sakhalin Island. This may be explained by either the postglacial recolonization of Kamchatka by larch that spread from Primor’e through Sakhalin and the Kuril Islands or its survival through the last glacial maximum in the Kamchatka Peninsula. The biogeography of larch and other woody plants indicate that boreal species have a common history of the colonization of Kamchatka.     

Allozyme Variation among Populations of Rana pirica (Amphibia: Anura)

Genetic variation of Rana pirica , an east Asian brown frog of the R. temporaria group, was elucidated by analysing 140 specimens from 11 populations from Hokkaido and Sakhalin, both locating near the eastern coasts of the Asian continent, and 12 specimens of R. ornativentris from Honshu, Japan mainland, as an outgroup, through horizontal starch gel electrophoresis. Rana pirica shows relatively low genetic differentiation, and high genetic affinities are found between Hokkaido and Sakhalin populations. Populations from these islands are morphologically somewhat differentiated but should be regarded as conspecific. Degree of genetic divergence among populations of amphibian species from Hokkaido, including R. pirica , is not so extensive as that reported for species from Japan mainland and relatively recent formation of amphibian fauna in Hokkaido is suggested.     

Genetic variations and phylogeography of the swallowtail butterfly Papilio machaon on the Japanese Islands

The swallowtail butterfly Papilio machaon Linnaeus, 1758 is widely distributed in the Holarctic region, including all of the main islands of Japan, as well as Sakhalin, and on other smaller islands south to Yakushima Island. The Japanese population is situated at the margin of the Eurasian distribution range of this species. It is morphologically different from other populations and has been classified as the subspecies hippocrates C. & R. Felder, 1864. The population of the Japanese Islands is considered to be genetically distinct from the continental populations in relation to the geographical history of the Japanese Islands. Therefore, we examined a part of the ND5 gene sequence of the mitochondrial DNA for P. machaon individuals of various localities in Japan and some nearby countries, and found 68 haplotypes in 400 individuals from the Japanese Islands and Sakhalin. A DNA polymorphism analysis revealed that the genetic structure of the Hokkaido population was significantly different from that of the southern populations on the main Japanese islands. These results imply that P. machaon expanded its range from the Amur region of Russia southward through Sakhalin to the Japanese Islands, and that the Tsugaru Strait between Hokkaido and Honshu may have subsequently limited their gene flow as a geographical barrier.     

Phylogeography of a northeast Asian spruce, Picea jezoensis, inferred from genetic variation observed in organelle DNA markers

Range-wide genetic variation of the widespread cold-temperate spruce Picea jezoensis was studied throughout northeast Asia using maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA markers. This study assessed 33 natural populations including three varieties of the species in Japan, Russia, China, and South Korea. We depicted sharp suture zones in straits around Japan in the geographical distribution pattern of mitochondrial haplotypes (GST=0.901; NST=0.934). In contrast, we detected possible extensive pollen flow without seed flow across the straits around Japan during the past population history in the distribution pattern of chloroplast haplotypes (GST=0.233; NST=0.333). The analysis of isolation by distance of the species implied that by acting as a barrier for the movement of seeds and pollen, the sharp suture zones contributed considerably to the level of genetic differentiation between populations. Constructed networks of mitochondrial haplotypes allowed inference of the phylogeographical history of the species. We deduced that the disjunction with Kamchatka populations reflects range expansion and contraction to the north of the current distribution. Within Japan, we detected phylogeographically different types of P. jezoensis between Hokkaido and Honshu islands; P. jezoensis in Honshu Island may have colonized this region from the Asian continent via the Korean peninsula and the species in Hokkaido Island is likely to have spread from the Asian continent via Sakhalin through land bridges. Japanese endemism of mitochondrial haplotypes in Hokkaido and Honshu islands might have been promoted by separation of these islands from each other and from the Asian continent by the straits during the late Quaternary.     

Notes on skulls of Pleistocene Saiga of Northern Eurasia

Eighteen fossil skulls of male Saiga from Northern Eurasia and 33 recent skulls from Kalmykia and Kazakhstan have been studied. Saiga from both the Khazarian Fauna of the Volga and Mammoth Fauna of Europe and Siberia are referred to Saiga horealis Tschersky, 1876. During the Pleistocene, 5. borealis distribution extended from England in the west to Alaska in the east and is characterized by an elongated neurocranium, small frontal angle of the temporal bone from the plane of the frontal, and long nasal bones.

S. borealis was a typical representative of the “mammoth biome”; in the Pleistocene periglacial steppes and cryogenic savannahs. Two subspecies are recognized: S. borealis borealis Tschersky (Eastern Sibera and Alaska); and S.b. prisca Nehring, 1891 (Europe, Urals and Western Siberia). At the end of the Pleistocene, when the mammoth disappeared, the range of S. borealis was reduced. Today they live only in West Mongolia (S. borealis mongolica Bannikov, 1946). S. tatarica tatarica was widely distributed in the other territories of the steppe and semidesert zones of Eurasia. The arid landscapes of Transcaucasia and Kazakhstan were inhabited by Saiga with thinner legs and shorter nasal bones, such as S. tatarica binagadensis Alekperova, 1953, from the middle Pleistocene of Azerbaijan (Bynagady). Fossil skulls from the Ural River that are large, but with a short neurocranium are identified as Saiga sp. cf. S. tatarica Linnaeus, 1766.     

Mitochondrial DNA variation pattern in larches of Eastern Siberia and the Far East

Genetic variation has been studied in 32 Eastern Siberian and Far Eastern populations of Larix Mill. with the use of three mitochondrial markers based on polymerase chain reaction. Eight multilocus haplotypes with a heterogeneous spatial distribution (G(ST) = 0.788, N(ST) = 0.829) have been found, which indicates limited gene flows between populations. Several geographic regions with specific larch haplotype sets have been determined: (1) Japan, (2) southern Sakhalin and the Kuril Islands, (3) Primor'e and Korea, (4) Kamchatka, and (5) Eastern Siberia and the northern Far East. The haplotype fixed in the Kamchatka is absent in the Magadan oblast or Chukotka but is present in southern Primor'e and Sakhalin Island. This may be explained by either the postglacial recolonization of Kamchatka by larch that spread from Primor'e through Sakhalin and the Kuril Islands or its survival through the last glacial maximum in the Kamchatka Peninsula. The biogeography of larch and other woody plants indicate that boreal species have a common history of the colonization of Kamchatka.     

Range-wide genetic structure in a north-east Asian spruce (Picea jezoensis) determined using nuclear microsatellite markers

Aim We used microsatellite markers to determine the range‐wide genetic structure of Picea jezoensis and to test the hypothesis that the past population history of this widespread cold‐temperate spruce has resulted in a low level of genetic variation and in imprints of inbreeding and bottlenecks in isolated marginal populations. Location The natural range of the three infraspecific taxa of P. jezoensis throughout north‐east Asia, including isolated marginal populations. Methods We analysed a total of 990 individuals across 33 natural populations using four nuclear microsatellite loci. Population genetic structure was assessed by analysing genetic diversity indices for each population, examining clustering (model‐based and distance‐based) among populations, evaluating signals of recent bottlenecks, and testing for isolation by distance (IBD). Results The 33 populations were clustered into five groups. The isolated marginal groups of populations (in Kamchatka, Kii in Japan and South Korea) exhibited low levels of allelic richness and gene diversity and a complete or almost complete loss of rare alleles. A recent bottleneck was detected in the populations in Hokkaido across to mid‐Sakhalin. The IBD analysis revealed that genetic divergence between populations was higher for populations separated by straits. Main conclusions Picea jezoensis showed a higher level of genetic differentiation among populations (F_ST = 0.101) than that observed in the genus Picea in general. This might be attributable to the fact that historically the straits around Japan acted as barriers to the movement of seeds and pollen. The low levels of genetic diversity in the isolated marginal population groups may reflect genetic drift that has occurred after isolation. Evidence of a significant bottleneck between the Hokkaido and mid‐Sakhalin populations implies that the cold, dry climate in the late Pleistocene resulted in the decline and contraction of populations, and that there was a subsequent expansion followed by a founder effect when conditions improved. The high polymorphism observed in P. jezoensis nuclear microsatellites revealed cryptic genetic structure that organellar DNA markers failed to identify in a previous study.     

Further Analysis of Intraspecific Sequence Variation of Chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): Implications for Biogeography of the Japanese Alpine Flora

Primula cuneifolia Ledeb. (Primulaceae), we analyzed intraspecific variation of the nucleotide sequences of non-coding regions of chloroplast DNA: the intergenic spacers between trnT (UGU) and the trnL (UAA) 5′exon, the trnL (UAA) 3′exon and trnF (GAA), and atpB and rbcL. In 20 populations of P. cuneifolia, 22 nucleotide substitutions and five insertions/deletions were inferred, and their genetic distances ranged from 0.001 to 0.008. Eight distinct haplotypes could be recognized and each haplotype was found to be geographically structured. Three major clades (the Northern, Hokkaido and Southern clades) were revealed in phylogenetic analyses of the haplotypes. The haplotypes of the Northern clade had a wider distribution area in the populations of Mt. Rausu and Rishiri Island of eastern and northern Hokkaido in Japan, northward to Unalaska Island in the Aleutians, and those of the Hokkaido clade were distributed in the populations of central Hokkaido and Mt. Iwaki of the northern Honshu in Japan; in addition, those of the Southern clade were observed only in the populations of the central Honshu. It was shown that the genetic diversifications of the Southern clade were higher than those of the Northern and Hokkaido clades. Furthermore, it was shown that the topology within the Southern clade was hierarchical, and the haplotypes of the Southern populations in the clade were derivative. From these results, we concluded that the cpDNA haplotypes of the three clades in P. cuneifolia arose and assumed the present distribution areas through several cycles of glacial advance and retreat in the Pleistocene. Received 24 June 1998/ Accepted in revised form 28 December 1998     

Description of a new species of Phylloscopus warbler from Vietnam and Laos

A new species of Phylloscopus warbler, which we name Phylloscopus calciatilis Limestone Leaf Warbler, is described from central and northern Vietnam and central and northern Laos; it probably also breeds in southernmost China. In morphology, the new species is very similar to Sulphur-breasted Warbler Phylloscopus ricketti , but it is smaller with a proportionately larger bill and rounder wing. Its song and calls are diagnostic. Based on mitochondrial and nuclear DNA, the new species is most closely related to P. ricketti and Yellow-vented Warbler Phylloscopus cantator , and it is inferred to be sister to the latter. The mitochondrial divergences between these three species are at the low end of the variation found in other species of Phylloscopus and Seicercus warblers, but greater than in other taxa generally treated as subspecies. Possible introgressive hybridization between the new species and P. ricketti is discussed, but more data are needed to establish whether it does occur and, if it does, to what extent. The new species appears to have a restricted breeding range in limestone karst environments, where it is locally common and therefore not under any immediate threat. In view of the recognition of the new species, all previous records of P. ricketti sensu lato need to be re-evaluated.     

Ancient Mitochondrial DNA Reveals the Origin of Sus scrofa from Rebun Island, Japan

The Kabukai A site (5 to 8C A.D.) of the Okhotsk cultural area is on Rebun Island, a small island near the coast, north–northwest of Hokkaido, Japan. Specimens of Sus scrofa, called the Sakhalin pig, were discovered in five cultural layers at the Kabukai A site. Ancient DNA was extracted from the remains of 42 Sakhalin pig bones. Thirty-nine nucleotide sequences of the 574-bp mitochondrial DNA control region, estimated to have originated from at least 21 individuals, were amplified and analyzed phylogenetically. Nine distinct haplotypes (A1, A2, A3, B1, B2, C1, C2, D1, and D2) from this site were classified into four haplotype groups (A, B, C, and D) by parsimonious network analysis. Phylogenetic analysis of 9 ancient and 55 modern haplotypes indicated that the population of Sakhalin pigs at the Kabukai A site belonged to two distinct clusters; haplotype groups A and B formed a cluster comprised only of themselves, and haplotype groups C and D belonged to the cluster of one of the two genetic groups of Japanese wild boars uniquely distributed in the western part of Japan, including one northeast Mongolian wild boar. Analysis of the haplotype distribution among three archaeological sites and their historical transitions among the five layers reflecting the cultural periods at the Kabukai A site suggests that the Sakhalin pig populations were introduced from Sakhalin island and the Amur River basin in the northeastern Eurasian continent together with some cultural influences. Received: 18 April 2000 / Accepted: 24 November 2000     

Phylogeographic Analysis of the Firefly, Luciola lateralis, in Japan and Korea Based on Mitochondrial Cytochrome Oxidase II Gene Sequences (Coleoptera: Lampyridae)

Luciola lateralis is widely distributed throughout the Korean Peninsula, northeast China, Sakhalin, and Japan. Two ecological types are recognized in Japan based on flash and hatching time characteristics. The mitochondrial cytochrome oxidase II gene was surveyed by restriction fragment length polymorphism analysis for Japan (46 populations) and Korea (two populations). Eleven haplotypes were detected. Gene trees revealed that haplotypes between Japan and Korea are much more differentiated in nucleotide sequences (8.1%) than those within Japan (0.3-1.4%) and Korea (0.7%). Haplotypes between Honshu and Hokkaido are not separated as clades, and the two ecological types cannot be segregated from each other phylogenetically. We suggest that the Japanese populations of this species may have dispersed within one million years ago and that ecological differences may be the result of physiological adaptation to cold climates.     

Phylogeography and demographic history of Siberian rubythroat <Emphasis Type="Italic">Luscinia calliope</Emphasis>

Phylogeographic analysis on the basis of individual marker variability provides insight into the history and mechanisms of the range formation of widely distributed species. A preliminary study of the mtDNA cytochrome b gene in Siberian rubythroat Luscinia calliope revealed the existence of three well-differentiated haplogroups, including one western and two eastern haplogroups. Continuing the study of the genetic markers of the species, we found that, in western part of the range, represented by the nominative geographic race, there were almost exclusively haplotypes of western group. In eastern populations of Khabarovsk krai, Chukotka, Kamchatka, and Sakhalin, haplotypes of all groups are mixed in different proportions. At the same time, the populations of Hokkaido and Iturup islands are exclusively represented by individuals with eastern haplotypes. Comparison of the identified nuclear copies of mitochondrial genes and construction of the phylogenetic network of haplotypes on the basis of cloned and initial sequences showed that two groups of eastern haplotypes (one of which geographically corresponded to L. c. anadyrensis and L. c. camtschatkensis and the second corresponded to L. c. sachalinensis) originated from nuclear pseudogenes of L. c. calliope through intergenomic recombination. In this regard, we propose a new hypothesis for the establishment of the modern range of this species, according to which the Siberian rubythroat dispersal from South Siberia occurred in two stages. At first, the species expanded its range to the northeast in the direction of the Kolyma and Koryak uplands. During the settling of these areas of northeastern Asia, a recombination between the mitochondrial and nuclear DNA took place, which led to the forming of a new haplotype, which was widespread in the emerging breeding populations. Birds with recombinant haplotypes populated the territories of Chukotka and Kamchatka, and then gradually occupied the Kuril Islands and, eventually, reached Hokkaido. At the next stage, Siberian rubythroat, probably, appeared in Sakhalin Island during spring migration, where some individuals stopped for breeding. Settling of the island was accompanied by similar intergenomic recombination and rapid fixation of a new recombinant haplotype with its subsequent spread across Sakhalin. The insular way of dispersal is completely repeated by modern migrants.     

Spawning behaviour of Sakhalin taimen, <Emphasis Type="Italic">Parahucho perryi</Emphasis>, from northern Hokkaido,Japan

A video camera mounted in an underwater housing and remotely operated was used to monitor the behaviour of five different Sakhalin taimen (Parahucho perryi), females and attendant males spawning in three coastal tributary streams in Northern Hokkaido, Japan. Based on three complete and two incomplete spawnings, we describe in detail for the first time the complete spawning behavioural repertoire of this species. The Sakhalin taimen was originally placed within Hucho, then removed from that genus based on morphological, life history and molecular data. Our study supports that removal—none of the behavioural traits we recorded clustered Parahucho with Hucho uniquely. Similarities between the two genera were all plesiomorphic traits that are widespread throughout the salmonines. The immediate behaviour right after spawning was found to be a major difference between Hucho and Parahucho. Like female Oncorhynchus and Salmo, Sakhalin taimen females cover their eggs by beats of their tails immediately after spawning. This is different from the “rest, then cover” behaviour shown by Siberian taimen (Hucho taimen) as well as lenok (Brachymystax lenok), supporting again that the Sakhalin taimen be removed from Hucho and placed in its own genus.