Phylogeography of Biomphalaria glabrata and B. pfeifferi, important intermediate hosts of Schistosoma mansoni in the New and Old World tropics

The historical phylogeography of the two most important intermediate host species of the human blood fluke Schistosoma mansoni, B. glabrata in the New World, and B. pfeifferi in the Old World, was investigated using partial 16S and ND1 sequences from the mitochondrial genome. Nuclear sequences of an actin intron and internal transcribed spacer (ITS)-1 were also obtained, but they were uninformative for the relationships among populations. Phylogenetic analyses based on mtDNA revealed six well-differentiated clades within B. glabrata: the Greater Antilles, Venezuela and the Lesser Antilles, and four geographically overlapping Brazilian clades. Application of a Biomphalaria-specific mutation rate gives an estimate of the early Pleistocene for their divergence. The Brazilian clades were inferred to be the result of fragmentation, due possibly to climate oscillations, with subsequent range expansion producing the overlapping ranges. Within the Venezuela and Lesser Antilles clade, lineages from each of these areas were estimated to have separated approximately 740 000 years ago. Compared to B. glabrata, mitochondrial sequences of B. pfeifferi are about 4x lower in diversity, reflecting a much younger age for the species, with the most recent common ancestor of all haplotypes estimated to have existed 880 000 years ago. The oldest B. pfeifferi haplotypes occurred in southern Africa, suggesting it may have been a refugium during dry periods. A recent range expansion was inferred for eastern Africa less than 100 000 years ago. Several putative species and subspecies, B. arabica, B. gaudi, B. rhodesiensis and B. stanleyi, are shown to be undifferentiated from other B. pfeifferi populations.     

Mitochondrial DNA variation and the phylogeography of the grey partridge (Perdix perdix) in Europe: from Pleistocene history to present day populations

Abstract For a phylogeographical analysis of European grey partridge (Perdix perdix) we sequenced 390 nucleotides of the 5′ end of the mitochondrial control region (CR) of 227 birds from several localities. The birds were divided into two major clades (western and eastern) which differed in control region 1 (CR1) by 14 nucleotide substitutions (3.6%). For estimation of the time of divergence, the whole CR of 14 specimens was sequenced. The major clades differed by 2.2%, corresponding to an estimated coalescence time of c. 1.1 million years. On CR1, 45 haplotypes were found. Western clade haplotypes were found in France, England, Germany, Poland, Italy and Austria. Eastern clade haplotypes were found in Finland, Bulgaria, Greece, and Ireland. One Finnish population and all Bulgarian and Irish populations were mixed, but only in Bulgaria was the mixing assumed to be natural. Nucleotide and haplotype diversities varied between populations, and both clades showed geographical structuring. The distribution of pairwise nucleotide differences in the eastern clade fitted the expectations of an expanding population. About 80% of the genetic structure in the grey partridge could be explained by the clades. The western clade presumably originates on the Iberian Peninsula (with related subtypes in Italy), and the eastern clade either on the Balkan or Caucasian refugia. Large‐scale hand‐rearing and releasing of western partridges have introduced very few mtDNA marks into the native eastern populations in Finland.     

Phylogenetic relationships among Hoplobatrachus rugulosus in Thailand as inferred from mitochondrial DNA sequences of the cytochrome-b gene (Amphibia, Anura, Dicroglossidae)

A fragment (564 bp) of the mitochondrial cytochrome-b (Cyt-b) gene was studied for 73 individual rice field frogs (Hoplobatrachus rugulosus) from 18 geographical locations (populations) within Thailand. Sequence analysis revealed the presence of 12 haplotypes, with five haplotypes being represented in two or more populations, and the other seven being population-distinct haplotypes. Phylogenetic analysis by maximum parsimony, maximum likelihood, and neighbor joining analyses all placed the 12 haplotypes into two distinct and well-separated clades with high bootstrap support, reflecting the high sequence divergences between the clades (25.3-32.3%). The mountain ranges and the Isthmus of Kra are likely to have played important roles in hindering gene flow among H. rugulosus populations in Thailand. From the sequence divergence values, the two clades of H. rugulosus can be classified into two distinct species, and therefore, the strains of H. rugulosus bred in farm stocks should be restricted to a population of one clade so as to avoid cross breeding between the two clades.     

The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations

The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species.     

Molecular Phylogeny and Genetic Divergence of the Introduced Populations of Japanese Guppies, Poecilia reticulata

A phylogenetic tree of guppies from seven introduced Japanese populations was constructed using a mitochondrial gene, and the relationship between these Japanese populations and indigenous South American populations was examined. Phylogenetic trees constructed by maximum parsimony and neighbor joining methods indicated four major groups: Group A: Trinidadian populations; Group B: the northernmost Okinawa populations; Group C: the northern Okinawa populations; Group D: Shimoda populations and the remainder of Trinidadian, Venezuelan, and southern Okinawa populations. Considerable genetic differences were observed among the haplotypes within each Okinawa population similar to that found among haplotypes of different native populations, but not within the Shimoda population, because each Okinawa population included haplotypes belonging to different groups. Genetic differences between Groups B, C, and D might reflect those of the introduced lineages; however, these differences might not result from the divergence after introduction events. These results suggested that multiple introductions of different breeding lineages might cause considerable divergence within and between Okinawa populations.     

Population genetic structure and the effect of founder events on the genetic variability of introduced sika deer, Cervus nippon, in Germany and Austria

The relationships among 214 wild-living sika deer from five locations in Germany and two in Lower Austria were examined using mitochondrial DNA (mtDNA) control region sequence. A total of 18 haplotypes are grouped consistently into two major divergent clades, A and B, which differ by a mean of 8.4% sequence divergence. Recently introduced sika deer showed a complex pattern of population structuring, which probably results from historical vicariance in at least two unknown source populations from southeastern Asia (as previously described by morphological and mtDNA findings), and subsequent population admixture as a result of human-mediated restocking. A strong genetic differentiation among populations was indicated by a global _ST value of 0.78 reflecting mainly the differential distribution of clades A and B haplotypes. There was no association between related haplotypes and their distribution among local populations. These indicate that genealogy is a better predictor of the genetic affinity among most sika deer populations than their present-day locations. The abundant mitochondrial divergence we observed, may reflect a subspecies differentiation and could be associated with phenotypic differences among the introduced sika deer.An erratum to this article can be found at     

DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes

European hedgehogs, Erinaceus europaeus and E. concolor, are among the many European plant and animal taxa that have been subjected to cyclical restriction to glacial refugia and interglacial expansion. An analysis of 95 mitotypes, comprising partial cytochrome b and control region sequences, shows deep divergence between the two hedgehog species. Three europaeus and two concolor clades are clearly identified and are consistent with previously identified refugia for Europe: the Iberian peninsula, Italy, and the Balkans. The degree of mitochondrial divergence among these clades suggests pre-Pleistocene separation of the refugial populations. In contrast, analysis of two nuclear introns clearly separates the two concolor clades, as in the mitochondrial data, but cannot discriminate the three europaeus clades. This discrepancy between nuclear and mitochondrial data is attributed to historical differences in the refugial population size of europaeus and concolor. The geographical distribution of mitotypes is analysed using nested clade analysis. This method, by including unobserved ('missing') mitotypes, can identify mitotype groupings that remain undetected in conventional analyses. However, the application of nested clade analysis to the study of refugial populations may be hampered by such factors as the loss of haplotypes from the refugial areas by repeated contractions of the population and the recent time scale of colonization relative to mutation rate.     

Postglacial colonisation patterns and the role of isolation and expansion in driving diversification in a passerine bird

Pleistocene glacial cycles play a major role in diversification and speciation, although the relative importance of isolation and expansion in driving diversification remains debated. We analysed mitochondrial DNA sequence data from 15 great reed warbler (Acrocephalus arundinaceus) populations distributed over the vast Eurasian breeding range of the species, and revealed unexpected postglacial expansion patterns from two glacial refugia. There were 58 different haplotypes forming two major clades, A and B. Clade A dominated in Western Europe with declining frequencies towards Eastern Europe and the Middle East, but showed a surprising increase in frequency in Western and Central Asia. Clade B dominated in the Middle East, with declining frequencies towards north in Central and Eastern Europe and was absent from Western Europe and Central Asia. A parsimonious explanation for these patterns is independent postglacial expansions from two isolated refugia, and mismatch distribution analyses confirmed this suggestion. Gene flow analyses showed that clade A colonised both Europe and Asia from a refugium in Europe, and that clade B expanded much later and colonised parts of Europe from a refugium in the Middle East. Great reed warblers in the eastern parts of the range have slightly paler plumage than western birds (sometimes treated as separate subspecies; A. a. zarudnyi and A. a. arundinaceus, respectively) and our results suggest that the plumage diversification took place during the easterly expansion of clade A. This supports the postglacial expansion hypothesis proposing that postglacial expansions drive diversification in comparatively short time periods. However, there is no indication of any (strong) reproductive isolation between clades and our data show that the refugia populations became separated during the last glaciation. This is in line with the Pleistocene speciation hypothesis invoking that much longer periods of time in isolation are needed for speciation to occur.     

Phylogeography and population structure of the Yunnan snub-nosed monkey (Rhinopithecus bieti) inferred from mitochondrial control region DNA sequence analysis

Rhinopithecus bieti, the Yunnan snub-nosed monkey, is the nonhuman primate with the highest altitudinal distribution and is also one of the 25 most globally endangered primate species. Currently, R. bieti is found in forests between 3000 and 4500 m above sea level, within a narrow area on the Tibetan Plateau between the Yangtze and Mekong rivers, where it is suffering from loss of habitat and shrinking population size (approximately 1500). To assess the genetic diversity within this species, its population structure and to infer its evolutionary history, we sequenced 401 bp of the hypervariable I (HVI) segment from the mitochondrial DNA control region (CR) for 157 individuals from 11 remnant patches throughout the fragmented distribution area. Fifty-two variable sites were observed and 30 haplotypes were defined. Compared with other primate species, R. bieti cannot be regarded as a taxon with low genetic diversity. Phylogenetic analysis partitioned haplotypes into two divergent haplogroups (A and B). Haplotypes from the two mitochondrial clades were found to be mixed in some patches although the distribution of haplotypes displayed local homogeneity, implying a strong population structure within R. bieti. Analysis of molecular variance detected significant differences among the different geographical regions, suggesting that R. bieti should be separated into three management units (MUs) for conservation. Based on our results, it can be hypothesized that the genetic history of R. bieti includes an initial, presumably allopatric divergence between clades A and B 1.0-0.7 million years ago (Ma), which might have been caused by the Late Cenozoic uplift of the Tibetan Plateau, secondary contact after this divergence as a result of a population expansion 0.16-0.05 Ma, and population reduction and habitat fragmentation in the very recent past.     

The interplay between habitat availability and population differentiation: a case study on genetic and morphological structure in an inland wader (Charadriiformes)

Long‐distance migrant waders breeding in the Arctic often have globally structured populations, largely because they were isolated in glacial or interstadial refugia or were restricted to fragmented coastal wetlands in winter. Conversely, inland species using continentally distributed wetlands appear to be less structured (more often panmictic), presumably because they are less likely to have been isolated by multiple refugia or by current events. We analyzed genetic variation in a widely distributed inland species, the ruff (Philomachus pugnax), sampled from seven Eurasian breeding localities, and from migration routes and wintering areas in Europe and Africa. One mitochondrial marker (N = 118) and eight nuclear microsatellites (N = 170) showed: (1) high genetic variation; (2) large genetic distances among mitochondrial (private) haplotypes within breeding populations; (3) the absence of a signature of isolation‐by‐distance; and (4) a distribution of private microsatellite alleles indicating dispersal between Scandinavia and Siberia but not between western and eastern Siberia. These results were consistent with a large refugial population during the Last Glacial Maximum, and postglacial long range expansions spreading ancestral polymorphisms, and not with a stepping‐stone model of gene flow. The divergence between breeding populations in Europe and Siberia was dated to approximately 12 000 years ago. Although genetic population structure is presently statistically non‐existent, support for evolving population structure came from analyses of geographical variation in two relevant phenotypic traits: wing length and the timing of migration. Analysis of 6077 individuals sampled on migration in 2002–08 revealed that, in each year, shorter‐winged birds migrated through significantly later than longer‐winged birds. The late‐passing birds were associated with more westerly breeding localities. In conclusion, the lack of genetic structuring in ruffs (and other inland species we examined) contrasts with strong structuring in many coastal species. This suggests that the ability to use more widely available inland habitat influences the evolution of genetic structure and the maintenance of genetic variation in waders. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 641–656.     

Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration

We analyzed sequences from a 275-bp hypervariable region in the 5' end of the mitochondrial DNA control region in 190 common chaffinches (Fringilla coelebs) from 19 populations in Europe and North Africa, including new samples from Greece and Morocco. Coalescent techniques were applied to estimate the time to the most recent common ancestor (TMRCA) and divergence times of these populations. The first objective of this study was to infer the locations of refugia where chaffinches survived the last glacial episode, and this was achieved by estimating the TMRCA of populations in regions surrounding the Mediterranean that were unglaciated in the late Pleistocene. Although extant populations in Iberia, Corsica, Greece, and North Africa harbor haplotypes that are basal in a phylogenetic tree, this information alone cannot be used to infer that these localities served as refugia, because it is impossible to infer the ages of populations and their divergence times without also considering the population genetic processes of mutation, migration, and drift. Provided we assume the TMRCAs of populations are a reasonable estimate of a population's age, coalescent-based methods place resident populations in Iberia, Corsica, Greece, and North Africa during the time of the last glacial maximum, suggesting these regions served as refugia for the common chaffinch. The second objective was to determine when populations began diverging from each other and to use this as a baseline to estimate current levels of gene flow. Divergence time estimates suggest that European populations began diverging about 60,000 years before present. The relatively recent divergence of populations in North Africa, Italy, and Iberia may explain why classic migration estimates based on equilibrium assumptions are high for these populations. We compare these estimates with nonequilibrium-based estimates and show that the nonequilibrium estimates are consistently lower than the equilibrium estimates.     

Phylogeny and biogeography of the alpine newt Mesotriton alpestris (Salamandridae, Caudata), inferred from mtDNA sequences

In this paper, we performed phylogenetic analyses of Mesotriton alpestris populations from the entire range of species distribution, using fragments of two mtDNA genes, cytochrome b (309bp) and 16S rRNA ( approximately 500bp). Sequence diversity patterns and phylogenetic analyses reveal the existence of a relict lineage (Clade A) of late Miocene origin, comprising populations from south-eastern Serbia. This lineage is proposed to be ancestor to a western and an eastern lineage, which diverged during the middle Pliocene. The western lineage is further divided in two clades (Clades B, C) of middle Pliocene origin that represent populations from Italy (B) and populations from central Europe and Iberia (C). Further subdivision, dated back to the middle-late Pliocene, was found within the eastern lineage, representing southern (Clade D) and central-northern (Clade E) Balkan populations, respectively. Extensive sequence divergence, implying greater isolation in multiple refugia, is found within eastern clades, while the western clades seem to have been involved in the colonization of central, western and north-eastern Europe from a hypothetical refugium in central Europe. The extent of divergence does not support the current taxonomy indicating cryptic speciation in the Balkans, while paedomorphic lineages were found to have been evolved during early-middle Pleistocene probably as a response to the ongoing dramatic climatic oscillations.     

Phylogeography of roe deer (Capreolus capreolus) populations: the effects of historical genetic subdivisions and recent nonequilibrium dynamics

We sequenced 704 mitochondrial DNA (mtDNA) control-region nucleotides and genotyped 11 autosomal microsatellites (STR) in 617 European roe deer (Capreolus capreolus) samples, aiming to infer the species' phylogeographical structure. The mtDNA sequences were split in three distinct haplogroups, respectively, named: Clade West, sampled mainly in Iberia; Clade East, sampled mainly in Greece and in the Balkans; and Clade Central, which was widespread throughout Europe, including the eastern countries and Iberia, but not Greece. These clades might have originated in distinct Iberian and Balkanic refuges during the penultimate or the last glaciations. Clades East and West contributed little to the current postglacial mtDNA diversity in central Europe, which apparently was recolonized mainly by haplotypes belonging to Clade Central. A unique subclade within Clade Central grouped all the haplotypes sampled from populations of the Italian subspecies C. c. italicus. In contrast, haplotypes sampled in central and southern Spain joined both Clade Central and Clade West, suggesting that subspecies C. c. garganta has admixed origin. STR data support a genetic distinction of peripheral populations in north Iberia and southern Italy, and show the effects of anthropogenic disturbance in fragmented populations, which were recently reintroduced or restocked and not may be in mutation-drift equilibrium. Roe deer in central Europe are mainly admixed, while peripheral populations in north Portugal, the southern Italian Apennines and Greece represent the remains of refugial populations and should be managed accordingly.     

Phylogeography of the fire-bellied toads Bombina: independent Pleistocene histories inferred from mitochondrial genomes

The fire-bellied toads Bombina bombina and Bombina variegata, interbreed in a long, narrow zone maintained by a balance between selection and dispersal. Hybridization takes place between local, genetically differentiated groups. To quantify divergence between these groups and reconstruct their history and demography, we analysed nucleotide variation at the mitochondrial cytochrome b gene (1096 bp) in 364 individuals from 156 sites representing the entire range of both species. Three distinct clades with high sequence divergence (K2P = 8-11%) were distinguished. One clade grouped B. bombina haplotypes; the two other clades grouped B. variegata haplotypes. One B. variegata clade included only Carpathian individuals; the other represented B. variegata from the southwestern parts of its distribution: Southern and Western Europe (Balkano-Western lineage), Apennines, and the Rhodope Mountains. Differentiation between the Carpathian and Balkano-Western lineages, K2P approximately 8%, approached interspecific divergence. Deep divergence among European Bombina lineages suggests their preglacial origin, and implies long and largely independent evolutionary histories of the species. Multiple glacial refugia were identified in the lowlands adjoining the Black Sea, in the Carpathians, in the Balkans, and in the Apennines. The results of the nested clade and demographic analyses suggest drastic reductions of population sizes during the last glacial period, and significant demographic growth related to postglacial colonization. Inferred history, supported by fossil evidence, demonstrates that Bombina ranges underwent repeated contractions and expansions. Geographical concordance between morphology, allozymes, and mtDNA shows that previous episodes of interspecific hybridization have left no detectable mtDNA introgression. Either the admixed populations went extinct, or selection against hybrids hindered mtDNA gene flow in ancient hybrid zones.     

Mitochondrial sequence analysis of Salamandra taxa suggests old splits of major lineages and postglacial recolonizations of central Europe from distinct source populations of Salamandra salamandra

Representatives of the genus Salamandra occur in Europe, Northern Africa and the Near East. Many local variants are known but species and subspecies status of these is still a matter of dispute. We have analysed samples from locations covering the whole expansion range of Salamandra by sequence analysis of mitochondrial D-loop regions. In addition, we have calibrated the rate of divergence of the D-loop on the basis of geologically dated splits of the closely related genus Euproctus. Phylogenetic analysis of the sequences suggests that six major monophyletic groups exist (S. salamandra, S. algira, S. infraimmaculata, S. corsica, S. atra and S. lanzai) which have split between 5 and 13 million years ago (Ma). We find that each of the Salamandra species occupies a distinct geographical area, with the exception of S. salamandra. This species occurs all over Europe from Spain to Greece, suggesting that it was the only species that has recolonized Central Europe after the last glaciation. The occurrence of specific east and west European haplotypes, as well as allozyme alleles in the S. salamandra populations suggests that this recolonization has started from at least two source populations, possibly originating in the Iberian peninsula and the Balkans. Two subpopulations of S. salamandra were found that are genetically very distinct from the other populations. One lives in northern Spain (S. s. bernardezi) and one in southern Italy (S. s. gigliolii). Surprisingly, the mitochondrial lineages of these subpopulations group closer together than the remainder S. salamandra lineages. We suggest that these populations are remnants of a large homogeneous population that had colonized Central Europe in a previous interglacial period, approximately 500 000 years ago. Animals from these populations were apparently not successful in later recolonizations. Still, they have maintained their separate genetic identity in their areas, although they are not separated by geographical barriers from very closely related neighbouring populations.     

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA

Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.     

Mitochondrial DNA structure and colony expansion dynamics of New Zealand fur seals (Arctocephalus forsteri) around Banks Peninsula

New Zealand fur seals are one of many pinniped species that survived the commercial sealing of the eighteenth and nineteenth centuries in dangerously low numbers. After the enforcement of a series of protection measures in the early twentieth century, New Zealand fur seals began to recover from the brink of extinction. We examined the New Zealand fur seal populations of Banks Peninsula, South Island, New Zealand using the mitochondrial DNA control region. We identified a panmictic population structure around Banks Peninsula. The most abundant haplotype in the area showed a slight significant aggregated structure. The Horseshoe Bay colony showed the least number of shared haplotypes with other colonies, suggesting a different origin of re-colonisation of this specific colony. The effective population size of the New Zealand fur seal population at Banks Peninsula was estimated at approximately 2500 individuals. The exponential population growth rate parameter for the area was 35, which corresponds to an expanding population. In general, samples from adjacent colonies shared 4.4 haplotypes while samples collected from colonies separated by between five and eight bays shared 1.9 haplotypes. The genetic data support the spill-over dynamics of colony expansion already suggested for this species. Approximate Bayesian computations analysis suggests re-colonisation of the area from two main clades identified across New Zealand with a most likely admixture coefficient of 0.41 to form the Banks Peninsula population. Approximate Bayesian computations analysis estimated a founder population size of approximately 372 breeding individuals for the area, which then rapidly increased in size with successive waves of external recruitment. The population of fur seals in the area is probably in the late phase of maturity in the colony expansion dynamic.     

Geographical segregation in Dunlin Calidris alpina populations wintering along the East Atlantic migratory flyway – evidence from mitochondrial DNA analysis

Dunlin Calidris alpina is one of the most abundant shorebirds using coastal habitats in the East Atlantic migratory flyway, that links arctic breeding locations (Greenland to Siberia) with wintering grounds (West Europe to West Africa). Differential migration and winter segregation between populations have been indicated by morphometrics and ringing recoveries. Here, we analyse the potential of genetic markers (mitochondrial DNA – mtDNA) to validate and enhance such findings. We compared mtDNA haplotypes frequencies at different wintering sites (from north-west Europe to West Africa). All birds from West Africa had western (European) haplotypes, while the eastern (Siberian) haplotypes were only present in European winter samples, reaching higher frequencies further north in Europe. Compilation of published results from migrating birds also confirmed these differences, with the sole presence of European haplotypes in Iberia and West Africa and increasingly higher frequencies of Siberian haplotypes from south-west to north-west Europe. Comparison with published haplotype frequencies of breeding populations shows that birds from Greenland, Iceland, and North Europe were predominant in wintering grounds in West Africa, while populations wintering in West Europe originated from more eastern breeding grounds (e.g. North Russia). These results show that genetic markers can be used to enhance the integrative monitoring of wintering and breeding populations, by providing biogeographical evidence that validate the winter segregation of breeding populations.     

Extensive gene flow within sibling species in the deep-sea fish Beryx splendens

Molecular markers allow insights into the population biology and ecology of deep-sea organisms, which are usually hardly accessible to direct observation and poorly known. Such a study was undertaken here for the deep-sea fish Beryx splendens, a species of growing interest to fisheries. B. splendens populations were sampled on seamounts and continental margins in the southwestern Pacific (New Caledonia, New Zealand, southeastern Australia) and in the northeastern Atlantic. Two hundred and fifty individuals were characterised by their single-strand DNA conformation (SSCP) of a approximately 360-base-pair (bp) fragment of the mitochondrial cytochrome b gene, amplified by the polymerase chain reaction (PCR). Two major SSCP haplotypes were observed in New Caledonia, a and w, whose frequencies were negatively correlated along a north-to-south cline. All SSCP haplotypes in the total sample were sequenced on 273 bp. The phylogenetic tree of B. splendens haplotype sequences, rooted by two B. decadactylus sequences, showed that a and w belong to distinct mitochondrial clades, A and W, which are separated by approximately 4-6% nucleotide divergence. Thirty individuals from New Caledonia were characterised by their DNA fingerprint from arbitrary-primed PCR. The distribution of individual-pairwise similarity indices was strongly bimodal. The larger similarity values all corresponded to comparisons within a clade (A or W) while the lower values were all between clades. Therefore, there was a strict association between the mitochondrial type and the DNA (presumably, nuclear DNA) fingerprint of an individual. Altogether, these results point to the existence of two biological species (sp. A and sp. W) within the current taxon B. splendens. No within-species differentiation was detected at the regional scale (New Caledonia). A remarkable result is that the three cytochrome b haplotypes of northeastern Atlantic B. cf. splendens sp. A were also the three commonest in the southwestern Pacific populations of this species. Such a level of homogeneity in the distribution of haplotypes suggests there is, or recently has been, gene flow at the inter-oceanic scale.     

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.