Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog,Nanorana yunnanensis (Dicroglossidae)

Historical drainage patterns adjacent to the Qinghai‐Tibetan Plateau differed markedly from those of today. We examined the relationship between drainage history and geographic patterns of genetic variation in the Yunnan spiny frog, Nanorana yunnanensis, using approximately 981 base pairs of mitochondrial DNA partial sequences from protein‐coding genes ND1 and ND2, and intervening areas including complete tRNA^Ile, tRNA^Gln and tRNA^Met. Two null hypotheses were tested: (i) that genetic patterns do not correspond to the development of drainage systems and (ii) that populations had been stable and not experienced population expansion, bottlenecking and selection. Genealogical analyses identified three, major, well‐supported maternal lineages, each of which had two sublineages. These divergent lineages were completely concordant with six geographical regions. Genetic structure and divergence were strongly congruent with historical rather than contemporary drainage patterns. Most lineages and sublineages were formed via population fragmentation during the rearrangement of paleodrainage basins in the Early Pliocene and Early Pleistocene. Sympatric lineages occurred only in localities at the boundaries of major drainages, likely reflecting secondary contact of previously allopatric populations. Extensive population expansion probably occurred early in the Middle Pleistocene accompanying dramatic climatic oscillations.     

Quaternary palaeoenvironmental oscillations drove the evolution of the Eurasian Carassius auratus complex (Cypriniformes,Cyprinidae)

Aim We sought to reconstruct the spatio‐temporal genetic diversification in goldfish of the Carassius auratus complex, which is widely distributed in Eurasia, to test whether vicariance events or human‐mediated translocations best explained lineage divergence and genogeographical history. Location East Asia and the Oriental islands including Japan, the Ryukyus and Taiwan, and Europe, including Russia and the Czech Republic. Methods We reconstructed the matrilineal history of Eurasian goldfish using 1876 sequences from the partial mitochondrial DNA control region (426 bp) and 191 complete sequences of cytochrome b (1140 bp) from 67 localities representing most of the range of the species. Divergence times were estimated using a Bayesian Markov chain Monte Carlo approach based either on molecular clock data or on the fossil record. Genetic structure and the historical demography of populations were analysed using partial correlation tests and analyses of molecular variance. Results Three lineages had high levels of regional specificity. Lineages A and B from the main islands of Japan differed greatly from lineage C, which occurred on the mainland, Taiwan and the Ryukyus. Lineages A and B had late Pliocene origins. Six geographically constrained sublineages within lineage C had near‐simultaneous mid‐Pleistocene divergences. Main conclusions Genetic structure in the C. auratus complex appears to have been driven by palaeoenvironmental perturbations rather than human translocations. The disappearance of a land bridge in the Tsushima Strait around 3.0 Ma is responsible for the separation of Japanese and continental lineages; the estimated divergence time is 2.75–2.32 Ma. Fujian, China and Vietnam appear to have provided important refugia for the C. auratus complex during glaciation. After warm, moist summer monsoons intensified during the mid‐Pleistocene, goldfish are likely to have dispersed north‐eastwards to recolonize the Ryukyus via Taiwan and northwards to recolonize mainland China.     

Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa

The recent discovery of cryptic species in marine holoplankton, organisms that 'drift' in oceanic currents throughout their life cycle, contrasts with their potential for long-distance passive dispersal and presumably high gene flow. These observations suggest that holoplankton species are adapting to surprisingly small-scale oceanographic features and imply either limited dispersal or strong selection gradients. Acartia tonsa is a widespread and numerically dominant estuarine copepod containing deep mitochondrial lineages within and among populations along the northwestern Atlantic coast. In this study, we intensively investigated A. tonsa populations in Chesapeake Bay with the goals of testing species status for the deep lineages and testing for their association with environmental features over space and time. Phylogenetic analyses of DNA sequences from mitochondrial cytochrome c oxidase I (mtCOI) and the nuclear ribosomal internal transcribed spacer (nITS) resolved two concordant monophyletic clades. Deep divergence between the two clades (13.7% uncorrected sequence divergence for mtCOI and 32.2% for nITS) and genealogical concordance within sympatric populations strongly suggest that the two clades represent reproductively isolated cryptic species. Based on restriction fragment length polymorphisms of mtCOI, representatives from the two clades were found consistently associated with contrasting salinity regimes (oligohaline vs. meso-polyhaline) with an overlap between 2 and 12 PSU in samples from 1995 to 2005. Finding these patterns in one of the best-known estuarine copepods reinforces the conclusion that marine biodiversity is underestimated, not only in terms of species numbers, but also with respect to niche partitioning and the potential importance of ecological divergence in marine holoplankton.     

Patterns of diversification in two species of short‐tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests

The small‐sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 527–539.     

Lineage divergence and speciation in the Web‐toed Salamanders (Plethodontidae: Hydromantes) of the Sierra Nevada,California

Peripatric speciation and the importance of founder effects have long been controversial, and multilocus sequence data and coalescent methods now allow hypotheses of peripatric speciation to be tested in a rigorous manner. Using a multilocus phylogeographical data set for two species of salamanders (genus Hydromantes) from the Sierra Nevada of California, hypotheses of recent divergence by peripatric speciation and older, allopatric divergence were tested. Phylogeographical analysis revealed two divergent lineages within Hydromantes platycephalus, which were estimated to have diverged in the Pliocene. By contrast, a low‐elevation species, Hydromantes brunus, diverged from within the northern lineage of H. platycephalus much more recently (mid‐Pleistocene), during a time of major climatic change in the Sierra Nevada. Multilocus species tree estimation and coalescent estimates of divergence time, migration rate, and growth rate reject a scenario of ancient speciation of H. brunus with subsequent gene flow and introgression from H. platycephalus, instead supporting a more recent divergence with population expansion. Although the small, peripheral distribution of H. brunus suggests the possibility of peripatric speciation, the estimated founding population size of the species was too large to have allowed founder effects to be important in its divergence. These results provide evidence for both recent speciation, most likely tied to the climatic changes of the Pleistocene, and older lineage divergence, possibly due to geological events, and add to evidence that Pleistocene glacial cycles were an important driver of diversification in the Sierra Nevada.     

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open‐ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite F_ST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.     

Persistent genetic signatures of historic climatic events in an Antarctic octopus

Repeated cycles of glaciation have had major impacts on the distribution of genetic diversity of the Antarctic marine fauna. During glacial periods, ice cover limited the amount of benthic habitat on the continental shelf. Conversely, more habitat and possibly altered seaways were available during interglacials when the ice receded and the sea level was higher. We used microsatellites and partial sequences of the mitochondrial cytochrome oxidase 1 gene to examine genetic structure in the direct‐developing, endemic Southern Ocean octopod Pareledone turqueti sampled from a broad range of areas that circumvent Antarctica. We find that, unusually for a species with poor dispersal potential, P. turqueti has a circumpolar distribution and is also found off the islands of South Georgia and Shag Rocks. The overriding pattern of spatial genetic structure can be explained by hydrographic (with ocean currents both facilitating and hindering gene flow) and bathymetric features. The Antarctic Peninsula region displays a complex population structure, consistent with its varied topographic and oceanographic influences. Genetic similarities between the Ross and Weddell Seas, however, are interpreted as a persistent historic genetic signature of connectivity during the hypothesized Pleistocene West Antarctic Ice Sheet collapses. A calibrated molecular clock indicates two major lineages within P. turqueti, a continental lineage and a sub‐Antarctic lineage, that diverged in the mid‐Pliocene with no subsequent gene flow. Both lineages survived subsequent major glacial cycles. Our data are indicative of potential refugia at Shag Rocks and South Georgia and also around the Antarctic continent within the Ross Sea, Weddell Sea and off Adélie Land. The mean age of mtDNA diversity within these main continental lineages coincides with Pleistocene glacial cycles.     

River islands,refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura,Ranidae) of the Qinghai‐Tibetan Plateau

Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai‐Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re‐treat to south‐eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG‐1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north‐eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.     

Inverted patterns of genetic diversity in continental and island populations of the heather Erica scoparia s.l.

Aim Using the heather Erica scoparia s.l. as a model, this paper aims to test theoretical predictions that island populations are genetically less diverse than continental ones and to determine the extent to which island and continental populations are connected by pollen‐ and seed‐mediated gene flow. Location Macaronesia, Mediterranean, Atlantic fringe of Europe. Methods Patterns of genetic diversity are described based on variation at two chloroplast DNA (cpDNA) loci and one nuclear DNA (nDNA) locus for 109 accessions across the entire distribution range of the species. Global patterns of genetic differentiation were investigated using principal coordinates analysis. Genetic differentiation between island and continental areas, estimations of pollen‐ and seed‐mediated gene flow, and the presence of phylogeographical signal were assessed by means of F_st /N_ST (continental scale) and F_ij/N_ij (local scale). Extant and past distribution ranges of the species were inferred from niche modelling using layers describing present and Last Glacial Maximum (LGM) macroclimatic conditions. Results The Azores exhibited a significantly higher genetic diversity than the continent. The lowest levels of genetic differentiation were observed between the Azores and the western Mediterranean, and the diversity observed in the Azores resulted from at least two colonization waves. Within the Azores, kinship coefficients showed a significant and much steeper decrease with geographical distance in the cpDNA than in the nDNA. The distribution predicted by LGM models was markedly different from the current potential distribution, particularly in western Europe, where no suitable areas were predicted by LGM models, and along the Atlantic coast of the African continent, where LGM models predicted highly suitable climatic conditions. Main conclusions The higher diversity observed in Azorean than in continental populations is inconsistent with MacArthur and Wilson’s equilibrium model and derived theoretical population genetic expectations. This inverted pattern may be the result of extinction on the continent coupled with multiple island colonization events and subsequent allopatric diversification and lineage hybridization in the Azores. The results highlight the role of allopatric diversification in explaining diversification on islands and suggest that this process has played a much more significant role in shaping Azorean biodiversity than previously thought.     

Molecular data and species distribution models reveal the Pleistocene history of the mayfly Ameletus inopinatus (Ephemeroptera: Siphlonuridae)1

1. We investigated the Pleistocene and Holocene history of the rare mayfly Ameletus inopinatus EATON 1887 (Ephemeroptera: Siphlonuridae) in Europe. We used A. inopinatus as a model species to explore the phylogeography of montane, cold‐tolerant aquatic insects with arctic–alpine distributions. 2. Using species distribution models, we developed hypotheses about the species demographic history in Central Europe and the recolonisation history of Fennoscandia. We tested these hypotheses using mitochondrial cytochrome oxidase I (mtCOI) sequence data and compared our genetic results with previously generated microsatellite data to explore genetic diversity distributions of A. inopinatus. 3. We observed old lineages, deep splits and almost complete lineage sorting of mtCOI sequences among mountain ranges. These results support a periglacial survival, i.e. persistence at the periphery of Pleistocene glaciers in Central Europe. 4. There was strong differentiation between the Fennoscandian and all other populations, indicating that Fennoscandia was recolonised from a refugium not accounted for in our sampling. High degrees of population genetic structure within the northern samples suggest that Fennoscandia was recolonised by more than one lineage. However, this structure was not apparent in previously published microsatellite data, consistent with secondary contact without sexual incompatibility or with sex‐biased dispersal. 5. Our demographic analyses indicate that (i) the separation of northern and Central European lineages occurred during the early Pleistocene; (ii) Central European populations have persisted independently throughout the Pleistocene and (iii) the species extended its range about 150 000 years ago.     

Discordant temporal and geographic patterns in maternal lineages of eastern North American frogs, Rana catesbeiana (Ranidae) and Pseudacris crucifer (Hylidae)

Whether the Pleistocene has had a disproportionate impact on the recent diversification of temperate species, or played a lesser role in a more protracted process, has been a prominent evolutionary debate for the past decade. We used cytochrome b sequences to reconstruct the evolutionary histories of two widely co-distributed, and ecologically divergent frogs (Rana catesbeiana and Pseudacris crucifer) to examine the role of the Pleistocene in structuring these species. Results for R. catesbeiana reflect a pattern of allopatric fragmentation, likely in Coastal Plain refugia on either side of the Mississippi River dating to the mid to early Pleistocene. In contrast, P. crucifer contains numerous divergent lineages, including one west of the Mississippi River in the Interior Highlands, and in the east, multiple lineages that likely expanded from a number of southern Appalachian refugia with lineage sundering originating in the late Pliocene. Large-scale phylogeographic comparisons between these and other eastern North American species reflect both congruent and independent patterns of diversification, possibly reflecting the relative importance of dispersal ability and habitat associations. Although intra-lineage diversification has been structured by repeated Pleistocene glaciations, lineage sundering likely dates at least to the Pliocene in most (but not all) northern temperate amphibian and reptile species studied to date.     

Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture data set and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male‐biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal‐biased X‐chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.     

Lineage diversification and historical demography of a sky island salamander,Plethodon ouachitae,from the Interior Highlands

Sky islands provide ideal opportunities for understanding how climatic changes associated with Pleistocene glacial cycles influenced species distributions, genetic diversification, and demography. The salamander Plethodon ouachitae is largely restricted to high‐elevation, mesic forest on six major mountains in the Ouachita Mountains. Because these mountains are separated by more xeric, low‐elevation valleys, the salamanders appear to be isolated on sky islands where gene flow among populations on different mountains may be restricted. We used DNA sequence data along with ecological niche modelling and coalescent simulations to test several hypotheses related to diversifications in sky island habitats. Our results revealed that P. ouachitae is composed of seven well‐supported lineages structured across six major mountains. The species originated during the Late Pliocene, and lineage diversification occurred during the Middle Pleistocene in a stepping stone fashion with a cyclical pattern of dispersal to a new mountain followed by isolation and divergence. Diversification occurred primarily on an east–west axis, which is likely related to the east–west orientation of the Ouachita Mountains and the more favourable cooler and wetter environmental conditions on north slopes compared to south‐facing slopes and valleys. All non‐genealogical coalescent methods failed to detect significant population expansion in any lineages. Bayesian skyline plots showed relatively stable population sizes over time, but indicated a slight to moderate amount of population growth in all lineages starting approximately 10 000–12 000 years ago. Our results provide new insight into sky island diversifications from a previously unstudied region, and further demonstrate that climatic changes during the Pleistocene had profound effects on lineage diversification and demography, especially in species from environmentally sensitive habitats in montane regions.     

Phylogeographic Patterns of mtDNA Variation Revealed Multiple Glacial Refugia for the Frog Species Feirana taihangnica Endemic to the Qinling Mountains

Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F _ct = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.     

Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii

The nature of population structure in microbial eukaryotes has long been debated. Competing models have argued that microbial species are either ubiquitous, with high dispersal and low rates of speciation, or that for many species gene flow between populations is limited, resulting in evolutionary histories similar to those of macroorganisms. However, population genomic approaches have seldom been applied to this question. Here, we analyse whole‐genome resequencing data for all 36 confirmed field isolates of the green alga Chlamydomonas reinhardtii. At a continental scale, we report evidence for putative allopatric divergence, between both North American and Japanese isolates, and two highly differentiated lineages within N. America. Conversely, at a local scale within the most densely sampled lineage, we find little evidence for either spatial or temporal structure. Taken together with evidence for ongoing admixture between the two N. American lineages, this lack of structure supports a role for substantial dispersal in C. reinhardtii and implies that between‐lineage differentiation may be maintained by reproductive isolation and/or local adaptation. Our results therefore support a role for allopatric divergence in microbial eukaryotes, while also indicating that species may be ubiquitous at local scales. Despite the high genetic diversity observed within the most well‐sampled lineage, we find that pairs of isolates share on average ~9% of their genomes in long haplotypes, even when isolates were sampled decades apart and from different locations. This proportion is several orders of magnitude higher than the Wright–Fisher expectation, raising many further questions concerning the evolutionary genetics of C. reinhardtii and microbial eukaryotes generally.     

Patterns and processes in the evolutionary history of parrotfishes (Family Labridae)

Phylogenetic reconstruction of the evolutionary relationships among 61 of the 70 species of the parrotfish genera Chlorurus and Scarus (Family Labridae) based on mitochondrial and nuclear gene sequences retrieved 15 well‐supported clades with mid Pliocene/Pleistocene diversification. Twenty‐two reciprocally monophyletic sister‐species pairs were identified: 64% were allopatric, and the remainder were sympatric. Age of divergence was similar for allopatric and sympatric species pairs. Sympatric sister pairs displayed greater divergence in morphology, ecology, and sexually dimorphic colour patterns than did allopatric pairs, suggesting that both genetic drift in allopatric species pairs and ecologically adaptive divergence between members of sympatric pairs have played a role in diversification. Basal species typically have small geographical ranges and are restricted to geographically and ecologically peripheral reef habitats. We found little evidence that a single dominant process has driven diversification, nor did we detect a pattern of discrete, sequential stages of diversification in relation to habitat, ecology, and reproductive biology. The evolution of Chlorurus and Scarus has been complex, involving a number of speciation processes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 529–557.     

Multiple Pleistocene refugia and post‐glacial colonization in the European chub (Squalius cephalus) revealed by combined use of nuclear and mitochondrial markers

Aim To analyse patterns of nuclear and mitochondrial genetic variation in the European chub, Squalius cephalus (Linnaeus, 1758), in order to understand the evolutionary history of this species and to test biogeographical hypotheses for the existence of co‐distributed European freshwater fish species. Location Rivers in Europe (Finland, Poland, Czech Republic, France, Bulgaria, Spain, Italy). Methods We genotyped 12 polymorphic microsatellite markers derived from 310 individuals collected from across the distribution of S. cephalus in Europe (including a total of 15 populations) and sequenced mitochondrial DNA (mtDNA) from a subset of 75 individuals. Sequences of mtDNA cytochrome b were analysed using both phylogenetic (median‐joining networks) and population genetic methods (tests for demographic history, mismatch distributions, Bayesian coalescent analysis). Geographical structure in microsatellite loci was examined using a distance method (F_ST), factorial correspondence analysis (FCA) and a Bayesian clustering method (structure ). Results The mtDNA network showed a clear split into four different haplogroup lineages: Western (separated into Atlantic and Danubian sublineages), Eastern, Aegean (occurring in two distinct sublineages in the Balkans and in Spain) and Adriatic. Our results indicate recent population expansion in the Eastern and Western Atlantic lineages and the admixture of two previously separate sublineages (Atlantic and Danubian) in the Western lineage. Bayesian structure analysis as well as FCA results roughly corresponded to the mtDNA‐based structure, separating the sampled individuals into almost non‐overlapping groups. Main conclusions Our results support hypotheses suggesting origins of extant lineages of freshwater fishes in multiple refugia and the subsequent post‐glacial colonization of Europe via different routes. We confirmed the previously proposed two‐step expansion scenario from the Danube refuge, the existence of a secondary (Atlantic) refuge during the last glaciation (probably in the Rhone River) and population expansion of this lineage. Conspicuous divergences among Mediterranean populations reflect their different origin, as well as their low contribution to the recent genetic pool of chub in central Europe.     

POPULATION STRUCTURE AND SPECIATION IN TROPICAL SEAS: GLOBAL PHYLOGEOGRAPHY OF THE SEA URCHIN DIADEMA

Abstract.— The causes of speciation in the sea are rarely obvious, because geographical barriers are not conspicuous and dispersal abilities or marine organisms, particularly those of species with planktonic larvae, are hard to determine. The phylogenetic relations of species in cosmopolitan genera can provide information on the likely mode of their formation. We reconstructed the phylogeny of the pantropical and subtropical sea urchin genus Diadema, using sequences of mitochondrial DNA from 482 individuals collected around the world, to determine the efficacy of barriers to gene flow and to ascertain the history of possible dispersal and vicariance events that led to speciation. We also compared 22 isozyme loci between all described species except D. palmeri. The mitochondrial DNA data show that the two deepest lineages are found in the Indian and West Pacific Oceans. (Indo‐Pacific) Diadema setosum diverged first from all other extant Diadema, probably during the initiation of wide fluctuations in global sea levels in the Miocene. The D. setosum clade then split 3‐5 million years ago into two clades, one found around the Arabian Peninsula and the other in the Indo‐West Pacific. On the lineage leading to the other species of Diadema, the deepest branch is composed of D. palmeri, apparently separated when the climate of New Zealand became colder and other tropical echinoids at these islands went extinct. The next lineage to separate is composed of a currently unrecognized species of Diadema that is found at Japan and the Marshall Islands. Diadema mexicanum in the eastern Pacific separated next, whereas D. paucispinum, D. savignyi, and D. antillarum from the western and central Atlantic, and (as a separate clade) D. antillarum from the eastern Atlantic form a shallow polytomy. Apparently, Indo‐Pacific populations of Diadema maintained genetic contact with Atlantic ones around the southern tip of Africa for some time after the Isthmus of Panama was complete. Diadema paucispinum contains two lineages: D. paucispinum sensu stricto is not limited to Hawaii as previously thought, but extends to Easter Island, Pitcairn, and Okinawa; A second mitochondrial clade of D. paucispinum extends from East Africa and Arabia to the Philippines and New Guinea. A more recent separation between West Indian Ocean and West Pacific populations was detected in D. setosum. Presumably, these genetic discontinuities are the result of water flow restrictions in the straits between northern Australia and Southeast Asia during Pleistocene episodes of low sea level. Diadema savignyi is characterized by high rates of gene flow from Kiribati in the central Pacific all the way to the East African Coast. In the Atlantic, there is a biogeographic barrier between the Caribbean and Brazil, possibly caused by fresh water outflow from the Amazon and the Orinoco Rivers. Diadema antillarum populations of the central Atlantic islands of Ascension and St. Helena are genetically isolated and phylogenetically derived from Brazil. Except for its genetic separation by the mid‐Atlantic barrier, Diadema seems to have maintained connections through potential barriers to dispersal (including the Isthmus of Panama) more recently than did Eucidaris or Echinometra, two other genera of sea urchins in which phylogeography has been studied. Nevertheless, the mtDNA phylogeography of Diadema includes all stages expected from models of allopatric differentiation. There are anciently separated clades that now overlap in their geographic distribution, clades isolated in the periphery of the genus range that have remained in the periphery, clades that may have been isolated in the periphery but have since spread towards the center, closely related clades on either side of an existing barrier, and closely related monophyletic entities on either side of an historical barrier that have crossed the former barrier line, but have not attained genetic equilibrium. Except for D. paucispinum and D. savignyi, in which known hybridization may have lodged mtDNA from one species into the genome of the other, closely related clades are always allopatric, and only distantly related ones overlap geographically. Thus, the phylogenetic history and distribution of extant species of Diadema is by and large consistent with allopatric speciation.     

The anatomy of a ‘suture zone’ in Amazonian butterflies: a coalescent‐based test for vicariant geographic divergence and speciation

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage‐specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance.     

Deep intra‐island divergence of a montane forest endemic: phylogeography of the Puerto Rican frog Eleutherodactylus portoricensis (Anura: Eleutherodactylidae)

Aim Hypotheses proposed for lineage diversification of tropical montane species have rarely been tested within oceanic islands. Our goal was to understand how basin barriers and Pleistocene climatic fluctuations shaped the distribution of diversity in Eleutherodactylus portoricensis (Eleutherodactylidae), a frog endemic to the montane rain forests of Puerto Rico. Location The north‐eastern (Luquillo) and south‐eastern (Cayey) mountains of Puerto Rico. Methods We generated mitochondrial DNA (mtDNA) control region sequences (c. 565 bp) from 144 individuals of E. portoricensis representing 16 localities, and sequenced 646 bp of cytochrome b and 596 bp of nuclear DNA (nDNA) rhodopsin exon and intron 1 from a subset of individuals. We conducted a phylogenetic analysis on the mtDNA sequence data and explored population substructure with maximum parsimony networks, a spatial analysis of molecular variance, and pairwise F_ST analysis. Coalescent simulations were performed to test alternative models of population divergence in response to late Pleistocene interglacial periods. Historical demography was assessed through coalescent analyses and Bayesian skyline plots. Results We found: (1) two highly divergent groups associated with the disjunct Luquillo and Cayey Mountains, respectively; (2) a shallow mtDNA genetic discontinuity across the La Plata Basin within the Cayey Mountains; (3) phylogeographic congruence between nDNA and mtDNA markers; (4) divergence dates for both mtDNA and nDNA pre‐dating the Holocene interglacial (c. 10 ka), and nDNA suggesting divergence in the penultimate interglacial (c. 245 ka); and (5) historical demographic stability in both lineages. Main conclusions The low‐elevation Caguas Basin is a long‐term barrier to gene flow between the two montane frog populations. Measures of genetic diversity for mtDNA were similar in both lineages, but lower nDNA diversity in the Luquillo Mountains lineage suggests infrequent dispersal between the two mountain ranges and colonization by a low‐diversity founder population. Population divergence began prior to the Holocene interglacial. Stable population sizes over time indicate a lack of demonstrable demographic response to climatic changes during the last glacial period. This study highlights the importance of topographic complexity in promoting within‐island vicariant speciation in the Greater Antilles, and indicates long‐term persistence and lineage diversification despite late Pleistocene climatic oscillations.