The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)

Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east-west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 +/- 0.76%, control region 6.7 +/- 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. F(ST) values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east-west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data.     

Marine biogeography of southern Australia: phylogeographical structure in a temperate sea-star

Aim To test whether marine biogeographical patterns observed at the community level are also important within species. It is postulated that historical hydrogeographic barriers have driven in situ diversification. Location The intertidal and shallow subtidal zones of southern Australia, New Zealand and nearby islands. Australia's temperate marine communities are characterized by a high degree of endemism and show strong biogeographical structure along an east–west axis. Methods Phylogeographical analysis of the widespread asteriid sea‐star Coscinasterias muricata Verrill across southern Australia and New Zealand. Forty‐two samples from 27 locations were included in phylogenetic analyses of mitochondrial (CO1; control region) and nuclear (ITS2) DNA sequences. Results Analysis of mtDNA revealed a deep phylogenetic split within Australian C. muricata, strongly correlated with latitude. ‘Northern’ haplotypes (latitude ≤ 37.6° S, nine sites, 15 samples) were 7.3–9.4% divergent from ‘southern’ haplotypes (latitude ≥ 37.6° S, 19 sites, 27 samples), consistent with late Pliocene separation. Eastern and western representatives of the ‘northern’ clade were 0.5–1.0% divergent, probably reflecting Pleistocene isolation. The ‘southern’ clade of Australia is also represented in New Zealand, indicating Pleistocene oceanic dispersal. Nuclear DNA (ITS2) sequences yielded relatively little phylogenetic resolution, but were generally congruent with mtDNA‐based groupings. Main conclusions The phylogeographical pattern detected within Australian C. muricata closely resembles marine biogeographical groupings proposed on the basis of community and species distributions. Recurring evolutionary patterns may have been driven by the hydrographic history of southern Australia. Specifically, we suggest that Plio‐Pleistocene temperature change and the repeated opening and closure of Bass Strait promoted allopatric divergence and perhaps cryptic speciation in C. muricata.     

Response of a southern temperate marsupial, the Tasmanian pademelon (Thylogale billardierii), to historical and contemporary forest fragmentation

Despite only limited Pleistocene glacial activity in the southern hemisphere, temperate forest species experienced complex distributional changes resulting from the combined effects of glaciation, sea level change and increased aridity. The effects of these historical processes on population genetic structure are now overlain by the effects of contemporary habitat modification. In this study, 10 microsatellites and 629 bp of the mitochondrial control region were used to assess the effects of historical forest fragmentation and recent anthropogenic habitat change on the broad-scale population genetic structuring of a southern temperate marsupial, the Tasmanian pademelon. A total of 200 individuals were sampled from seven sites across Tasmania and two islands in Bass Strait. High mitochondrial and nuclear genetic diversity indicated the maintenance of large historical population sizes. There was weak phylogeographical structuring of haplotypes, although all King Island haplotypes and three Tasmanian haplotypes formed a divergent clade implying the mid-Pleistocene isolation of a far northwestern population. Both the mitochondrial and nuclear data indicated a division of Tasmanian populations into eastern and western regions. This was consistent with a historical barrier resulting from increased aridity in the lowland 'midlands' region during glacial periods, and with a contemporary barrier resulting from recent habitat modification in that region. In Tasmania, gene flow appears to have been relatively unrestricted during glacial maxima in the west, while in the east there was evidence for historical expansion from at least one large glacial refuge and recolonization of Flinders Island.     

When east meets west: population structure of a high-latitude resident species,the boreal chickadee (Poecile hudsonicus)

The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60–96 kya. Pairwise F_ST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r²=0.51) than for microsatellites (r²=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.     

Contrasting genetic structuring between colonies of the World’s smallest penguin, <Emphasis Type="Italic">Eudyptula minor</Emphasis> (Aves: Spheniscidae)

The Little Penguin, Eudyptula minor, is a seabird that nests in colonies throughout New Zealand and southern Australia. Individuals from different colonies in southeast Australia differ significantly in morphology and ecology, suggesting that some genetic structuring may exist among colonies. In contrast, the marking of individuals with flipper bands has revealed some, albeit infrequent, movement between colonies. To determine the extent of genetic structuring, we tested the null hypothesis of substantial gene flow within southeast Australia by examining patterns of genetic variation across seven colonies separated by up to 1,500 km. Phylogeographic structuring was absent for mitochondrial control region sequences (2–3 individuals per colony). Microsatellite allele frequencies at five loci and mitochondrial haplotype frequencies (50 individuals per colony) were also homogenous among the majority of colonies sampled, although two colonies at the western periphery of the sampling range were distinct from those to the east. The genetic homogeneity among the majority of colonies can be explained by low but consistent contemporary gene flow among them, or a recent founder event in Bass Strait following the last marine transgression. The genetic break towards the western end of the sampling distribution appears best explained by differences in sea surface temperature and, consequentially breeding phenology, the latter hindering genetically effective migration.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Concordant mitochondrial and microsatellite DNA structuring between Polish lowland and Carpathian Mountain wolves

Phylogeographic studies of highly mobile large carnivores suggest that intra-specific genetic differentiation of modern species might be the consequence of the most recent Pleistocene glaciation. However, the relative influence of biogeographical processes and subsequent human-induced population fragmentation requires a better understanding. Poland represents the western edge of relatively continuous distributions of many wide-ranging species, e.g. lynx (Lynx lynx), wolves (Canis lupus), moose (Alces alces) and, therefore, a key area for understanding historic and contemporary patterns of gene flow in central Europe. We examined wolf genetic structure in Poland and in a recently recolonized area in eastern Germany using microsatellite profiles (n = 457) and mitochondrial DNA sequencing (mtDNA, n = 333) from faecal samples. We found significant genetic structure and high levels of differentiation between wolves in the Carpathian Mountains and the Polish lowlands. Our findings are consistent with previously reported mtDNA subdivision between northern lowlands and southern mountains, and add new and concordant findings based on autosomal marker variation. Wolves in western Poland and eastern Germany showed limited differentiation from northeastern Poland. Although the presence of private alleles suggests immigration also from areas not sampled in this study, most individuals seem to be immigrants from northeastern Poland or their descendants. We observed moderate genetic differentiation between certain northeastern lowland regions separated by less than 50 km. Moreover, mtDNA results indicated a southeastern subpopulation near the border with Ukraine. The observed structure might reflect landscape fragmentation and/or ecological differences resulting in natal habitat-biased dispersal.     

Phylogeographical disjunction in abundant high-dispersal littoral gastropods

Abstract Phylogeographical disjunctions in high-dispersal marine taxa are variously ascribed to palaeogeographical conditions or contemporary ecological factors. Associated biogeographical studies, however, seldom incorporate the sampling design required to confidently discriminate among such competing hypotheses. In the current study, over 7800 gastropod specimens were examined for operculum colour, and 129 specimens genetically, to test ecological and historical biogeographical hypotheses relating to biogeographical disjunction in the Southern Hemisphere, and to southern Australia in particular. Mitochondrial DNA sequence analysis of the high-dispersal intertidal gastropod Nerita atramentosa in southern Australia (88 specimens; 18 localities) revealed an east-west phylogeographical split involving two highly divergent clades (26.0 +/- 1.9%) exhibiting minimal geographical overlap in the southeast. The eastern clade of Nerita atramentosa is also widespread in northern New Zealand (43 specimens, 10 localities), but no significant genetic differentiation is explained by the Tasman Sea, a 2000-km-wide oceanic barrier. Spatial genetic structure was not detected within either clade, consistent with the species' dispersive planktotrophic phase lasting for 5-6 months. Digital analysis of operculum colouration revealed substantial differences between eastern (tan) and western (black) specimens. Genetic analysis and visual inspection of 88 Australian specimens revealed a completely nonrandom association between mtDNA data and operculum colouration. Independent examination of a further 7822 specimens from 14 sites in southern Australia revealed both colour morphs at all localities, but reinforced the phylogeographical data by indicating a marked turnover in colour morph abundance associated with a palaeogeographical barrier: Wilsons Promontory. This sharp biogeographical disjunction is in marked contrast to the species' high dispersal abilities. The genetic similarity of Nerita morio (Easter Island) and the eastern Australian + New Zealand lineage (1.1 +/- 0.3%) provides further evidence of long-distance dispersal in southern Nerita. Phylogenetic relationships of nine species (four genera) of Neritidae, an almost exclusively tropical gastropod family, are consistent with the hypothesis that southern temperate black nerites comprise a monophyletic radiation.     

Landscape discontinuities influence gene flow and genetic structure in a large, vagile Australian mammal, Macropus fuliginosus

Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.     

Contemporary population structure and post‐glacial genetic demography in a migratory marine species,the blacknose shark,Carcharhinus acronotus

Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear‐encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Bay of Campeche in the southern Gulf of Mexico and the Bahamas. Pairwise estimates of genetic divergence between sharks in the Bahamas and those in all other localities were more than an order of magnitude higher than between pairwise comparisons involving the other localities. Demographic modelling indicated that sharks in all five regions diverged after the last glacial maximum and, except for the Bahamas, experienced post‐glacial, population expansion. The patterns of genetic variation also suggest that the southern Gulf of Mexico may have served as a glacial refuge and source for the expansion. Results of the study demonstrate that barriers to gene flow and historical genetic demography contributed to contemporary patterns of population structure in a coastal migratory species living in an otherwise continuous marine habitat. The results also indicate that for many marine species, failure to properly characterize barriers in terms of levels of contemporary gene flow could in part be due to inferences based solely on equilibrium assumptions. This could lead to erroneous conclusions regarding levels of connectivity in species of conservation concern.     

The imprint of Quaternary glaciers on the present-day distribution of the obligate groundwater amphipod Niphargus virei (Niphargidae)

Aim A plausible yet untested biogeographical scenario suggests that Quaternary glaciers shaped the present‐day distribution of the groundwater amphipod Niphargus virei. This study was designed to test two hypotheses pertaining to this scenario: (1) the probability of occurrence of N. virei in ice‐free areas decreases in the vicinity of the Würm glacier; and (2) dispersal is sufficiently low for the historical record of glacial effects to persist over time. Location The study area was located in the southern Jura Mountains, France. Methods A total of 497 sites were sampled to ascertain the distribution of N. virei in the southern Jura. Amplified fragment length polymorphism was analysed from a subset of 24 sites. The relationships between the probability of occurrence of N. virei and distance to the Würm glacier or elevation were investigated using a logistic regression. Spatial autocorrelation analyses were performed on both the residuals of the logistic regression and genetic distance to test the significance of dispersal and barriers to post‐glacial recolonization. The influence of catchment boundaries as barriers to dispersal was examined using different neighbouring relationships between sites. We tested the statistical significance of the reduction in deviance and gain in precision of an autologistic regression that took into consideration the influence of dispersal constraints on the distribution of N. virei. Results Niphargus virei rarely occurred in formerly glaciated areas, and its probability of occurrence in ice‐free areas decreased in the vicinity of the Würm glacier. Combined autocorrelation analyses of spatial distribution and spatial genetic structure showed that: (1) the distance at which spatial autocorrelation was no longer significantly positive did not exceed 16 km; (2) genetic differentiation fitted a model of isolation by distance; and (3) catchment boundaries acted as barriers to dispersal. The autologistic regression with dispersal constraints significantly increased our capacity to predict the distribution of N. virei. Maps of probabilities of occurrence suggested that post‐glacial recolonization was impeded by the extension of glacial outwash. Main conclusions The present distribution of N. virei in southern Jura is probably the result of a historical range reduction driven by glaciation coupled with restricted dispersal and isolation by distance.     

Dispersal vs. vicariance in the Mediterranean: historical biogeography of the Palearctic Pachydeminae (Coleoptera, Scarabaeoidea)

Aim The geological evolution of the Mediterranean region is largely the result of the Tertiary collision of the African and Eurasian Plates, but also a mosaic of migrating island arcs, fragmenting tectonic belts, and extending back‐arc basins. Such complex paleogeography has resulted in a ‘reticulate’ biogeographical history, in which Mediterranean biotas repeatedly fragmented and merged as dispersal barriers appeared and disappeared through time. In this study, dispersal‐vicariance analysis (DIVA) is used to assess the relative role played by dispersal and vicariance in shaping distribution patterns in the beetle subfamily Pachydeminae Reitter, 1902 (Scarabaeoidea), an example of east–west Mediterranean disjunction. Location The Mediterranean region, including North Africa, the western Mediterranean, Balkans–Anatolia, Middle East, Caucasus, the Iranian Plateau, and Central Asia. Methods A phylogenetic hypothesis of the Palearctic genera of Pachydeminae in conjunction with distributional data was analysed using DIVA. This method reconstructs the ancestral distribution in a given phylogeny based on the vicariance model, while allowing dispersal and extinction to occur. Unlike other methods, DIVA does not enforce area relationships to conform to a hierarchical ‘area cladogram’, so it can be used to reconstruct ‘reticulate’ biogeographical scenarios. Results Optimal reconstructions, requiring 23 dispersal events, suggest that the ancestor of Pachydeminae was originally present in the south‐east Mediterranean region. Basal splitting within the subfamily was caused by vicariance events related to the late Tertiary collision of the African microplates Apulia and Arabia with Eurasia, and the resultant arise of successive dispersal barriers (e.g. the Red Sea, the Zagros Mountains). Subsequent diversification in Pachydeminae involved multiple speciation events within the Middle East and Iran–Afghanistan regions, which gave rise to the least speciose genera of Pachydeminae (e.g. Otoclinius Brenske, 1896). Finally, the presence of Pachydeminae in the western Mediterranean region seems to be the result of a recent dispersal event. The ancestor of the Iberian genera Ceramida Baraud, 1987 and Elaphocera Gené, 1836 probably dispersed from the Middle East to the Iberian Peninsula across North Africa and the Gibraltar Strait during the ‘Messinian salinity crisis’ at the end of the Miocene. Main conclusions Although the basal diversification of Pachydeminae around the Mediterranean appears to be related to vicariance events linked to the geological formation of the Mediterranean Basin, dispersal has also played a very important role. Nearly 38% of the speciation events in the phylogeny resulted from dispersal to a new area followed by allopatric speciation between lineages. Relationships between western and eastern Mediterranean disjuncts are usually explained by dispersal through Central Europe. The biogeographical history of the Pachydeminae corroborates other biogeographical studies that consider North Africa to be an alternative dispersal route by which Mediterranean taxa could have achieved circum‐Mediterranean distributions.     

Triton's trident: cryptic Neogene divergences in a marine clam (Lasaea australis) correspond to Australia's three temperate biogeographic provinces

The southern coast of Australia is composed of three distinct biogeographic provinces distinguished primarily by intertidal community composition. Several ecological mechanisms have been proposed to explain their formation and persistence, but no consensus has been reached. The marine clam Lasaea australis is arguably the most common bivalve on southern Australian rocky shores and occurs in all three provinces. Here, we tested if this species exhibits cryptic genetic structuring corresponding to the provinces and if so, what mechanisms potentially drove its divergence. Variation in two mitochondrial genes (16S and COIII) and one nuclear gene (ITS2) was assayed to test for genetic structuring and to reconstruct the clam's phylogenetic history. Our results showed that L. australis is comprised of three cryptic mitochondrial clades, each corresponding almost perfectly to one of the three biogeographic provinces. Divergence time estimates place their cladogenesis in the Neogene. The trident‐like topology and Neogene time frame of L. australis cladogenesis are incongruent with Quaternary vicariance predictions: a two‐clade topology produced by Pleistocene Bass Strait land bridge formation. We hypothesize that the interaction of the Middle Miocene Climate Transition with the specific geography of the southern coastline of Australia was the primary cladogenic driver in this clam lineage. Additional in‐depth studies of the endemic southern Australian marine biota across all three provinces are needed to establish the generality of this proposed older framework for regional cladogenesis.     

Islands within an island: Population genetic structure of the endemic Sardinian newt,Euproctus platycephalus

The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus. Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male‐biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island‐restricted amphibians, especially in the context of disease and climate change.     

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush‐tailed rock‐wallaby (Petrogale penicillata; n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush‐tailed rock‐wallabies, whose divergence appears to date to the mid‐Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north–south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush‐tailed rock‐wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.     

Complex phylogeography in the Southern Smooth Snake (Coronella girondica) supported by mtDNA sequences

Palearctic reptiles with wide distribution through the Western Mediterranean are expected to display genetic substructuring because of the combining effects of current or past geographic barriers and climate fluctuations. We have examined this issue by sequencing cytochrome b and 16S rRNA mitochondrial fragments of 80 individuals of the snake Coronella girondica from 71 localities, covering the range of the species across Tunisia, Algeria, Morocco, Spain, Portugal, southern France and north‐western Italy. According to the obtained genealogy, C. girondica is structured into three divergent and well‐supported clades (north‐western Africa, Betic range and Iberia–France–Italy), which greatly match other phylogeographies already published for this region. Our estimations suggest that the divergence among the three clades took place approximately 1.4‐2.0 Ma, which roughly coincides with the Plio‐Pleistocene transition, characterized by an increase in climate variability. The existence of a clade in a narrow belt of south‐eastern Iberia represents another example of the high endemism rate of the region, with a key geographical situation and an important role in vicariant processes. Since the split among the three major lineages would be take place after the opening of the Strait of Gibraltar, overwater dispersal is here suggested. The subsequent genetic substructuring of these clades during the Pleistocene fits within the refugia‐within‐refugia model, highlighting the importance of the region as a scenario for multiple vicariant events.     

Distribution patterns of the genus Pacifigorgia (Octocorallia: Gorgoniidae): track compatibility analysis and parsimony analysis of endemicity

Aim We analysed the distribution patterns of the eastern Pacific octocoral genus Pacifigorgia and deduced its ancestral distribution to determine why Pacifigorgia is absent from the Gulf of Mexico, the Caribbean of central America, and the Antilles. We also examined the current patterns of endemism for Pacifigorgia to look for congruence between hot spots of endemism in the genus and generally recognized areas of endemism for the eastern Pacific. Location The tropical eastern Pacific and western Atlantic, America. Methods We used track compatibility analysis (TCA) and parsimony analysis of endemicity (PAE) to derive ancestral distribution patterns and hot spots of endemism, respectively. Distributional data for Pacifigorgia were gathered from several museum collections and from fieldwork, particularly in the Pacific of Costa Rica and Panama. Results A single generalized track joined the three main continental eastern Pacific biogeographical provinces and the western Atlantic. This track can be included within a larger eastern Atlantic–eastern Pacific transoceanic track that may be the oldest transoceanic track occurring in the region. PAE results designate previously recognized eastern Pacific biogeographical provinces as Pacifigorgia hot spots of endemism. The number of endemic species, which for other taxonomic groups is similar among the eastern Pacific provinces, is higher in the Panamic province for Pacifigorgia. Main conclusions We propose that the absence of Pacifigorgia from the Gulf of Mexico, the Caribbean of central America, and the Antilles is the result of an ancient absence of the genus from these areas rather than the consequence of a major, recent, extinction episode. The Cortez province and the Mexican province appear together as a result of either non‐response to vicariance or dispersal across the Sinaloan Gap. We posit that the Central American Gap acts as a barrier that separates the Panamic province from the northern Cortez–Mexican province.     

Across the southern Andes on fin: glacial refugia,drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re‐colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro‐glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic → Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.     

Phylogeography of the eight-barbel loach <Emphasis Type="Italic">Lefua nikkonis</Emphasis> (Cypriniformes: Nemacheilidae): how important were straits in northern Japan as biogeographical barriers?

Many straits in the Japanese archipelago have been proposed as biogeographical boundaries, but there is disagreement regarding their importance as historic barriers against dispersal of terrestrial and freshwater taxa. Mitochondrial DNA haplotype and phylogenetic analyses of Lefua nikkonis, a primary freshwater fish inhabiting northern Japan and descendent from Siberia, revealed that the species is genetically structured within its geographic range, but that two major haplotypes are widely distributed across the Ishikari Lowland of Hokkaido Island as well as across the Tsugaru Strait between Hokkaido and Honshu Islands, two well-known biogeographical boundaries of northern Japan. The two major haplotypes were separated from each other by only one mutational step, and many other haplotypes, including those endemic to the region south of these barriers, have diverged from the major haplotypes, suggesting rapid range expansion and local differentiation. Divergence-time estimates, based on vicariance of the Honshu endemic congener L. echigonia via uplift of the Central Highlands, demonstrated that the southward dispersal of L. nikkonis from Hokkaido Island to Honshu Island occurred less than 0.08–0.19 Mya, suggesting that a land bridge emerged at the Tsugaru Strait during the Riss glaciation. Given that other freshwater taxa crossed the strait earlier (during the Middle Pleistocene), it is likely that land bridges in the strait have repeatedly emerged. The fact that L. nikkonis invaded only the northern part of Honshu, and that many other freshwater species also have the limit of their distribution ranges in this area as well, indicates that a faunal transition zone might persist even without the Tsugaru Strait. Thus, straits and lowlands in northern Japan are likely to have been less important as dispersal barriers to freshwater taxa than is currently thought.     

East–west genetic differentiation in Musk Ducks (<Emphasis Type="Italic">Biziura lobata</Emphasis>) of Australia suggests late Pleistocene divergence at the Nullarbor Plain

Musk Ducks (Biziura lobata) are endemic to Australia and occur as two geographically isolated populations separated by the Nullarbor Plain, a vast arid region in southern Australia. We studied genetic variation in Musk Duck populations at coarse (eastern versus western Australia) and fine scales (four sites within eastern Australia). We found significant genetic structure between eastern and western Australia in the mtDNA control region (Φ_ST = 0.747), one nuclear intron (Φ_ST = 0.193) and eight microsatellite loci (F_ST = 0.035). In contrast, there was little genetic structure between Kangaroo Island and adjacent mainland regions within eastern Australia. One small population of Musk Ducks in Victoria (Lake Wendouree) differed from both Kangaroo Island and the remainder of mainland eastern Australia, possibly due to genetic drift exacerbated by inbreeding and small population size. The observed low pairwise distance between the eastern and western mtDNA lineages (0.36%) suggests that they diverged near the end of the Pleistocene, a period characterised by frequent shifts between wet and arid conditions in central Australia. Our genetic results corroborate the display call divergence and Mathews’ (Austral Avian Record 2:83–107, 1914) subspecies classification, and confirm that eastern and western populations of Musk Duck are currently isolated from each other.