Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes

The phylogeographical patterns and population genetic structures of Varicorhinus barbatulus in Taiwan were investigated based on genetic diversity of 34 allozyme loci and nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mtDNA. Allozyme and mtDNA analyses revealing evident geographical structuring suggest limited gene flow between populations (F(ST)=0.511 and 0.791, respectively). Low genetic variability within populations (P=5.56%; He=0.018) based on allozymes and significantly negative Tajima's D statistics based on mtDNA suggest that most populations in Taiwan may have originated from a small number of founders followed by demographic expansion. The gene genealogy of mtDNA identified six lineages corresponding to major drainages that were separated by the geological barriers due to vicariant events. A minimum spanning network based on nucleotide substitutions reflects divergence from populations of the Miao-li Plateau to northern and southern regions of the island. In contrast to a previous hypothesis that suggests an early invasion to eastern part of Taiwan prior to the lifting of central mountain range some one million years ago, the mtDNA genealogy and molecular dating reveal very recent colonization of the eastern population. Nested clade analyses revealing significant associations between genetic structure and geographical division identify past fragmentation and range expansion as major phylogeographical events that shaped the geographical distribution of this species in Taiwan.     

Phylogeography of southern Asian Dolly Varden char <Emphasis Type="Italic">Salvelinus malma krascheninnikovi</Emphasis>: Genealogical analysis of mitochondrial DNA

Phylogeography of southern Asian Dolly Varden char was studied using the data on mtDNA variation (regions ND1/ND2, ND5/ND6, and Cytb/D loop) obtained using PCR-RFLP analysis. Analysis of contemporary population genetic structure showed that Salvelinus malma krascheninnikovi throughout the whole species range was characterized by high population differentiation in combination with rather small differences between the populations from remote regions. The genealogy of mtDNA haplotypes was reconstructed and nested clade analysis of geographical distances was performed. Geographical distribution of mtDNA haplotypes of S. m. krascheninnikovi was explained by population genetic processes (restricted gene flow), as well as by historical demographic events (range expansion and fragmentation). It was demonstrated that the main demographic events were associated with cyclic processes of the geological formation of the Sea of Japan and adjacent territories. Furthermore, genealogical tree of S. m. krascheninnikovi contained the traces of secondary contact between isolated phylogeographical lineages.     

Comparative phylogeography of the two pink salmon broodlines: an analysis based on a mitochondrial DNA genealogy

Over most of their natural northern Pacific Ocean range, pink salmon (Oncorhynchus gorbuscha) spawn in a habitat that was repeatedly and profoundly affected by Pleistocene glacial advances. A strictly two-year life cycle of pink salmon has resulted in two reproductively isolated broodlines, which spawn in alternating years and evolved as temporal replicates of the same species. To study the influence of historical events on phylogeographical and population genetic structure of the two broodlines, we first reconstructed a fine-scale mtDNA haplotype genealogy from a sample of 80 individuals and then determined the geographical distribution of the major genealogical assemblages for 718 individuals sampled from nine Alaskan and eastern Asian even- and nine odd-year pink salmon populations. Analysis of restriction site states in seven polymerase chain reaction (PCR)-amplified mtDNA regions (comprising 97% of the mitochondrial genome) using 13 endonucleases resolved 38 haplotypes, which clustered into five genealogical lineages that differed from 0.065 to 0.225% in net sequence divergence. The lineage sorting between broodlines was incomplete, which suggests a recent common ancestry. Within each lineage, haplotypes exhibited star-like genealogies indicating recent population growth. The depth of the haplotype genealogy is shallow ( approximately 0.5% of nucleotide sequence divergence) and probably reflects repeated decreases in population size due to Pleistocene glacial advances. Nested clade analysis (NCA) of geographical distances showed that the geographical distribution observed for mitochondrial DNA (mtDNA) haplotypes resulted from alternating influences of historical range expansions and episodes of restricted dispersal. Analyses of molecular variance showed weak geographical structuring of mtDNA variation, except for the strong subdivision between Asian and Alaskan populations within the even-year broodline. The genetic similarities observed among and within geographical regions probably originated from postglacial recolonizations from common sources rather than extensive gene flow. The phylogeographical and population genetic structures differ substantally between broodlines. This can be explained by stochastic lineage sorting in glacial refugia and perhaps different recolonization routes in even- and odd-year broodlines.     

Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.     

Phylogeography of a salmonid fish,masu salmon Oncorhynchus masou subspecies-complex,with disjunct distributions across the temperate northern Pacific

1. Climate oscillations during the Pleistocene had profound effects on the evolutionary history of freshwater fishes now distributed across northern temperate regions. The extent of continental glaciation on the western side of the North Pacific, including areas of East Asia, was more limited as compared with regions of North America, Europe and high-latitude areas of the North Pacific. Therefore, the effects of climate oscillations might have influenced species in dissimilar ways depending on the species' distribution.
2. We used mitochondrial DNA (mtDNA) and microsatellite DNA (msDNA) markers to clarify the evolutionary history of masu salmon Oncorhynchus masou subspecies-complex (family Salmonidae) distributed in historically non-glaciated regions in the western North Pacific.
3. No marked regional or subspecies-specific mtDNA haplotype associations were recognised, except for O. masou subsp., a lacustrine form endemic to Lake Biwa, an ancient lake in central Honshu. The landlocked subspecies O. masou formosanus, with a disjunct distribution on Taiwan Island, exhibited no diagnostic population features differing from the other subspecies, in either mtDNA or msDNA markers. Mismatch distribution and Bayesian skyline plot analyses indicated relatively recent range expansion and rapid population growth for masu salmon during the last glacial period (c. 0.1–0.15 Ma).
4. Contrary to the mtDNA genealogy, Bayesian clustering using msDNA showed two main genetic clusters, mainly northern populations of the subspecies O. m. masou and populations of the subspecies O. m. ishikawae in southern areas of the Japanese Archipelago. Notably, O. m. formosanus on Taiwan Island was included in the O. m. masou group, and O. masou subsp. was included in the O. m. ishikawae group.
5. Our results suggest that the masu salmon subspecies-complex in historically non-glaciated regions of the Temperate Northern Pacific is characterised by weak population structuring and shallow genetic differentiation among the subspecies, except for O. masou subsp. owing to its long isolation in Lake Biwa. Incomplete lineage sorting and historical inter-subspecies hybridisation, possibly due to secondary contact, seem to be plausible explanations for discrepancies in the mitochondrial DNA genealogy and nuclear DNA genetic structure.

     

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.     

中国狼不同地理种群遗传多样性及系统进化分析

为了解中国狼不同地理种群遗传多样性及系统发育情况,从中国境内狼的主要分布区青海、新疆、内蒙古和吉林4个地区采集样品,用分子生物学技术手段成功地获得44个个体线粒体DNA控制区第一高变区(HVRⅠ)序列和40个线粒体Cyt b部分序列。线粒体控制区HVRⅠ共检测到51个变异位点,位点变异率为8.76%;线粒体Cyt b部分序列发现31个变异位点,位点变异率为5.33%,未见插入及缺失现象,变异类型全部为碱基置换。共定义了16个线粒体HVRⅠ单倍型,其中吉林与内蒙种群存在共享单倍型,估计这两地间种群亲缘关系较近。4个地理种群中新疆种群拥有较高的遗传多样性(0.94)。中国狼种群总体平均核苷酸多态性为2.27%,与世界其他国家地区相比,中国狼种群拥有相对较高的遗传多样性。通过线粒体HVRⅠ单倍型构建的系统进化树可以看出,中国狼在进化上分为2大支,其中位于青藏高原的青海种群独立为一支,推测其可能长期作为独立种群进化。基于青海种群与新疆,内蒙种群的线粒体Cyt b遗传距离,推测中国狼2个世系可能在更新世冰川时期青藏高原受地质作用急速隆起后出现分歧,分歧时间大约在1.1 MY前。     

Population structure of <Emphasis Type="Italic">Nouelia insignis</Emphasis> (Asteraceae), an endangered species in southwestern China,based on chloroplast DNA sequences: recent demographic shrinking

Nouelia insignis, an endangered species, is distributed in the Jinsha and Nanpan drainage areas in southwestern China. In this study, we examined the genetic diversity and population structure based on the sequences of the cpDNA rpL 16 intron. Low levels of genetic variation were detected within all populations of the endemic species. A gene genealogy of 11 haplotypes recovered two major lineages I and II, with haplotypes H1 and H6 nested as interior nodes, respectively. Haplotype H1 was widespread in all populations, while haplotype H6 was restricted to populations southern of the Jinsha River. Low levels of genetic differentiation were detected, as most F _st values between populations were zero. This result, however, contradicts previous studies based on allozymes and fingerprinting. Genetic analyses suggested that coancestry due to low evolutionary rates resulted in the lack of geographical subdivision. Molecular dating estimated that the two lineages split about 3.224 MYA (95% CI 1.070–6.089 MYA). Maintenance of ancestral polymorphisms was possibly attributable to a long-standing large effective population size until recently. Postglacial demographic expansion was supported by a unimodal mismatch distribution and star-like phylogenies.     

Cryptic diversity in the mtDNA of the ornamental fish Carnegiella strigata

Mitochondrial DNA ( mtDNA) sequences of the marbled hatchetfish Carnegiella strigata, an ornamental fish exported from the Negro River, was examined to determine its genetic diversity and population structure in blackwater rivers (Negro and Uatumã Rivers) in the central Amazon. Analyses of a 646 bp fragment of the ATPase 6/8 mtDNA gene revealed two monophyletic lineages of C. strigata with considerable genetic distance between them (10–12%), suggesting that these lineages should not be considered a single stock. Furthermore, there were strong differences in the geographical distribution of the lineages. These results indicate a past association between drainages of the Negro and Uatumã Rivers. They also suggest that, in the Negro River, its main tributary, the Branco River, may act as a geographical barrier and potentially an ecological barrier between populations of the middle and lower portions of the river.     

Mitochondrial DNA variation in natural populations of endangered Indian Feather-Back Fish, Chitala chitala

Genetic variation at mitochondrial cytochrome b (cyt b) and D-loop region reveals the evidence of population sub-structuring in Indian populations of highly endangered primitive feather-back fish Chitala chitala. Samples collected through commercial catches from eight riverine populations from different geographical locations of India were analyzed for cyt b region (307 bp) and D-loop region (636–716 bp). The sequences of the both the mitochondrial regions revealed high haplotype diversity and low nucleotide diversity. The patterns of genetic diversity, haplotypes networks clearly indicated two distinct mitochondrial lineages and mismatch distribution strongly suggest a historical influence on the genetic structure of C. chitala populations. The baseline information on genetic variation and the evidence of population sub-structuring generated from this study would be useful for planning effective strategies for conservation and rehabilitation of this highly endangered species.     

Genetic population structure of the paper wasp Polistes olivaceus (Hymenoptera: Vespidae) in Bangladesh

Dispersal triggers gene flow, which in turn strongly affects the ensuing genetic population structure of a species. Using nuclear microsatellite loci and mitochondrial DNA (mtDNA), we estimated the genetic population structure of the wasp Polistes olivaceus throughout Bangladesh. The level of population differentiation using nuclear markers (F _ST) appeared to be much lower than that estimated using mtDNA haplotype sequences (Ф_ST), even after correcting for effective population size differences between the two markers. These results suggest a philopatric tendency, in which gynes disperse less than males. We observed no isolation by distance among the study populations at either the nuclear or mtDNA level, suggesting nonequilibrium between gene flow and drift as a result of very frequent interpopulation movement. For the nuclear markers, an individual assignment test showed no genetically and geographically distinct groups. Instead, phylogenetic analyses as well as a minimum spanning network using mtDNA haplotypes consistently revealed two distinct lineages. The distribution of haplotypes indicated western populations with a single lineage and offered clear evidence for restricted gene flow across the Jamuna–Padma–Upper Meghna river system. Mismatch distributions exhibited a unimodal distribution, which along with a starlike haplotype network, suggested a population expansion in lineage I but not in lineage II. Overall, these results suggest that gene flow among populations of P. olivaceus was affected by both female philopatry and a major river system across Bangladesh.     

Incomplete barriers to mitochondrial gene flow between pheromone races of the North American pine engraver,Ips pini (Say) (Coleoptera,Scolytidae)

The pine engraver Ips pini (Say) is known to include three pheromone races, but gene flow between these races has not been investigated. We used maternally inherited mitochondrial DNA (mtDNA) variation to infer gene flow between 22 widely distributed North American populations of I. pini for a total of 217 individuals, based on 354 bp of the cytochrome oxidase I gene. Gene flow was estimated cladistically as migrants per generation (Nm) and as haplotype variation between populations (N_st). Three distinct mtDNA haplotype lineages, generally corresponding to eastern (I), Rocky Mountain (II) and western (III) regions of North America, were resolved with a total of 34 distinct I. pini haplotypes. The distributions of these lineages were largely congruent with the geographical ranges of the ''New York'', ''California'' and ''Idaho–Montana'' pheromone races. Only individuals with lineage I mtDNA were observed among eastern populations, whereas individuals with lineage II or III mtDNA predominated among western populations. Gene flow (Nm and N_st) was generally moderate between all populations. However, the presence of lineage I mtDNA on the eastern side of western North America and the absence of lineage II and III mtDNA in eastern North America suggest directional gene flow from east to west. These results indicate that female-controlled assortative mating among pheromone races may disrupt gene flow between conspecifics, reflecting incomplete pre-mating barriers.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

Haplotype Frequency Distribution in Northeastern European Saduria entomon (Crustacea: Isopoda) Populations. A Phylogeographic Approach

The distribution pattern of mtDNA haplotypes in distinct populations of the glacial relict crustacean Saduria entomon was examined to assess phylogeographic relationships among them. Populations from the Baltic, the White Sea and the Barents Sea were screened for mtDNA variation using PCR‐based RFLP analysis of a 1150 bp fragment containing part of the CO I and CO II genes. Five mtDNA haplotypes were recorded. An analysis of geographical heterogeneity in haplotype frequency distributions revealed significant differences among populations. The isolated populations of S. entomon have diverged since the retreat of the last glaciation. The geographical pattern of variation is most likely the result of stochastic (founder effect, genetic drift) mechanisms and suggests that the haplotype differentiation observed is probably older than the isolation of the Baltic and Arctic seas.     

Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan

The genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population harboring the lineage A mitochondria expanded in the recent past, while lineage B showed weak signals of a population expansion. It is not clear whether the two lineages of mtDNA evolved in separate or identical geographical regions. We discuss two hypotheses regarding the two lineages of mtDNA: a cryptic race/species hypothesis and a selective sweep hypothesis.     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

Molecular population genetics of the red kangaroo (Macropus rufus): mtDNA variation

The genetic population structure of a large, wide-ranging marsupial, the red kangaroo ( Macropus rufus ) was assessed using sequence and haplotype frequency data of mitochondrial DNA (mtDNA) from locations across the species range in Australia. Results from sequence data revealed extensive haplotype diversity within the red kangaroo (32/34 sequences were unique). Sequence diversity was distributed within rather than between geographical regions across the species range. Genetic connectivity across the range of the species has therefore been maintained over the long term. On a smaller within-region scale, significant genetic structuring was evident from heterogeneity of haplotype frequencies amongst sampling sites. The geographical scale of panmictic populations differed across the continent with more restricted genetic populations occurring in areas with greater topographic and habitat complexity. We propose that these differences in area of genetic populations are the result of population responses to limiting ecological factors during drought.     

MITOCHONDRIAL DNA VARIATION IN THE FIELD VOLE (MICROTUS AGRESTIS): REGIONAL POPULATION STRUCTURE AND COLONIZATION HISTORY

Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.     

Extinction and recolonization of maritime Antarctica in the limpet Nacella concinna (Strebel, 1908) during the last glacial cycle: toward a model of Quaternary biogeography in shallow Antarctic invertebrates

Quaternary glaciations in Antarctica drastically modified geographical ranges and population sizes of marine benthic invertebrates and thus affected the amount and distribution of intraspecific genetic variation. Here, we present new genetic information in the Antarctic limpet Nacella concinna, a dominant Antarctic benthic species along shallow ice‐free rocky ecosystems. We examined the patterns of genetic diversity and structure in this broadcast spawner along maritime Antarctica and from the peri‐Antarctic island of South Georgia. Genetic analyses showed that N. concinna represents a single panmictic unit in maritime Antarctic. Low levels of genetic diversity characterized this population; its median‐joining haplotype network revealed a typical star‐like topology with a short genealogy and a dominant haplotype broadly distributed. As previously reported with nuclear markers, we detected significant genetic differentiation between South Georgia Island and maritime Antarctica populations. Higher levels of genetic diversity, a more expanded genealogy and the presence of more private haplotypes support the hypothesis of glacial persistence in this peri‐Antarctic island. Bayesian Skyline plot and mismatch distribution analyses recognized an older demographic history in South Georgia. Approximate Bayesian computations did not support the persistence of N. concinna along maritime Antarctica during the last glacial period, but indicated the resilience of the species in peri‐Antarctic refugia (South Georgia Island). We proposed a model of Quaternary Biogeography for Antarctic marine benthic invertebrates with shallow and narrow bathymetric ranges including (i) extinction of maritime Antarctic populations during glacial periods; (ii) persistence of populations in peri‐Antarctic refugia; and (iii) recolonization of maritime Antarctica following the deglaciation process.