Comparative molecular phylogeography of North American softshell turtles (Apalone): implications for regional and wide-scale historical evolutionary forces

We use a comparative analysis of partial cytochrome b sequences to evaluate the evolutionary forces shaping wide-scale phylogeographic patterns of all three North American softshell turtles (Apalone ferox, A. mutica, and A. spinifera). The overall phylogeographic patterns are concordant with results from both extensive regional studies of southeastern species, implicating historical vicariant processes during the Pliocene and Pleistocene, and investigations of more northerly distributed species, indicating a bottleneck effect of recent dispersal into postglacial habitat. We also resolved a novel, shared genetic break between northern-western and southeastern populations within both A. mutica and A. spinifera, demonstrating the value of using widespread taxa to evaluate both regional and wider scale phylogeographic patterns. The extensive phylogenetic structure and sequence divergences within both A. mutica and A. spinifera contrast sharply with most previous studies of turtles and with the hypothesis that turtles in general have slow rates of mtDNA evolution.     

Large-scale phylogeography of the disjunct Neotropical tree species Schizolobium parahyba (Fabaceae-Caesalpinioideae)

Neotropical rainforests exhibit high levels of endemism and diversity. Although the evolutionary genetics of plant diversification has garnered increased interest, phylogeographic studies of widely distributed species remain scarce. Here we describe chloroplast and nuclear variation patterns in Schizolobium parahyba (Fabaceae), a widespread tree in Neotropical rainforests that harbor two varieties with a disjunct distribution. Chloroplast and nuclear sequence analyses yielded 21 and 4 haplotypes, respectively. Two genetic diversity centers that correlate with the two known varieties were identified: the Southeastern Atlantic forest and the Amazonian basin. In contrast, the populations from southern and northeastern Atlantic forests and Andean-Central American forests exhibited low levels of genetic diversity and divergent haplotypes, likely related to historical processes that impact the flora and fauna in these regions, such as a founder's effect after dispersion and demographic expansion. Phylogeographic and demographic patterns suggest that episodes of genetic isolation and dispersal events have shaped the evolutionary history for this species, and different patterns have guided the evolution of S. parahyba. Moreover, the results of this study suggest that the dry corridor formed by Cerrado and Caatinga ecoregions and the Andean uplift acted as barriers to this species' gene flow, a picture that may be generalized to most of the plant biodiversity tropical woodlands and forests. These results also reinforce the importance of evaluating multiple genetic markers for a more comprehensive understanding of population structure and history. Our results provide insight into the conservation efforts and ongoing work on the genetics of population divergence and speciation in these Neotropical rainforests.     

Comparative phylogeography and demographic history of the wood lemming (Myopus schisticolor): implications for late Quaternary history of the taiga species in Eurasia

The association between demographic history, genealogy and geographical distribution of mitochondrial DNA cytochrome b haplotypes was studied in the wood lemming (Myopus schisticolor), a species that is closely associated with the boreal forest of the Eurasian taiga zone from Scandinavia to the Pacific coast. Except for a major phylogeographic discontinuity (0.9% nucleotide divergence) in southeastern Siberia, only shallow regional genetic structure was detected across northern Eurasia. Genetic signs of demographic expansions imply that successive range contractions and expansions on different spatial scales represented the primary historical events that shaped geographical patterns of genetic variation. Comparison of phylogeographic structure across a taxonomically diverse array of other species that are ecologically associated with the taiga forest revealed similar patterns and identified two general aspects. First, the major south-north phylogeographic discontinuity observed in five out of six species studied in southeastern Siberia and the Far East implies vicariant separation in two different refugial areas. The limited distribution range of the southeastern lineages provides no evidence of the importance of the putative southeastern refugial area for postglacial colonization of northern Eurasia by boreal forest species. Second, the lack of phylogeographic structure associated with significant reciprocal monophyly and genetic signatures of demographic expansion in all nine boreal forest animal species studied to date across most of northern Eurasia imply contraction of each species to a single refugial area during the late Pleistocene followed by range expansion on a continental scale. Similar phylogeographic patterns observed in this taxonomically diverse set of organisms with different life histories and dispersal potentials reflect the historical dynamics of their shared environment, the taiga forest in northern Eurasia.     

Phylogeography and demographic history of the neotropical otter (Lontra longicaudis)

The Neotropical otter (Lontra longicaudis) is a medium-sized semiaquatic carnivore with a broad distribution in the Neotropical region. Despite being apparently common in many areas, it is one of the least known otters, and genetic studies on this species are scarce. Here, we have investigated its genetic diversity, population structure, and demographic history across a large portion of its geographic range by analyzing 1471 base pairs (bp) of mitochondrial DNA from 52 individuals. Our results indicate that L. longicaudis presents high levels of genetic diversity and a consistent phylogeographic pattern, suggesting the existence of at least 4 distinct evolutionary lineages in South America. The observed phylogeographic partitions are partially congruent with the subspecies classification previously proposed for this species. Coalescence-based analyses indicate that Neotropical otter mitochondrial DNA lineages have shared a rather recent common ancestor, approximately 0.5 Ma, and have subsequently diversified into the observed phylogroups. A consistent scenario of recent population expansion was identified in Eastern South America based on several complementary analyses of historical demography. The results obtained here provide novel insights on the evolutionary history of this largely unknown Neotropical mustelid and should be useful to design conservation and management policies on behalf of this species and its habitats.     

Pleistocene phylogeographic effects on avian populations and the speciation process.

Pleistocene biogeographic events have traditionally been ascribed a major role in promoting speciations and in sculpting the present-day diversity and distributions of vertebrate taxa. However, this paradigm has recently come under challenge from a review of interspecific mtDNA genetic distances in birds: most sister-species separations dated to the Pliocene. Here we summarize the literature on intraspecific mtDNA phylogeographic patterns in birds and reinterpret the molecular evidence bearing on Pleistocene influences. At least 37 of the 63 avian species surveyed (59%) are sundered into recognizable phylogeographic units, and 28 of these separations (76%) trace to the Pleistocene. Furthermore, use of phylogroup separation times within species as minimum estimates of ''speciation durations'' also indicates that many protracted speciations, considered individually, probably extended through time from Pliocene origins to Pleistocene completions. When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier. Whether the Pleistocene was exceptional in these regards compared with other geological times remains to be determined.     

Phylogenetic and phylogeographic analysis of the genus Orestias (Teleostei: Cyprinodontidae) in the southern Chilean Altiplano: the relevance of ancient and recent divergence processes in speciation

This study presents phylogenetic molecular data of the Chilean species of Orestias to propose an allopatric divergence hypothesis and phylogeographic evidence that suggests the relevance of abiotic factors in promoting population divergence in this complex. The results reveal that diversification is still ongoing, e.g. in the Ascotán salt pan, where populations of Orestias ascotanensis restricted to individual freshwater springs exhibit strong genetic differentiation, reflecting putative independent evolutionary units. Diversification of Orestias in the southern Altiplano may be linked to historical vicariant events and contemporary variation in water level; these processes may have affected the populations from the Plio‐Pleistocene until the present.     

Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood, and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best‐fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best‐fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers. In contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features and more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.     

Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna

The phylogenetic relationships within the piranhas were assessed using mitochondrial sequences with the aim of testing several hypotheses proposed to explain the origin of Neotropical diversity (palaeogeography, hydrogeology and museum hypotheses). Sequences of the ribosomal 16S gene (510 bp) and control region (980 bp) were obtained from 15 localities throughout the main South American rivers for 21 of the 28 extant piranha species. The results indicate that the genus Serrasalmus is monophyletic and comprises three major clades. The phylogeographical analyses of these clades allowed the identification of five vicariant events, extensive dispersal and four lineage duplications suggesting the occurrence of sympatric speciation. Biogeographical patterns are consistent with the prediction made by the museum hypothesis that lineages from the Precambrian shields are older than those from the lowlands of the Amazon. The vicariant events inferred here match the distribution of the palaeoarches and several postdispersal speciation events are identified, thereby matching the predictions of the palaeogeography and hydrogeology hypotheses, respectively. Molecular clock calibration of the control region sequences indicates that the main lineages differentiated from their most recent common ancestor at 9 million years ago in the proto Amazon-Orinoco and the present rate of diversification is the highest reported to date for large carnivorous Characiformes. The present results emphasize that an interaction among geology, sea-level changes, and hydrography created opportunities for cladogenesis in the piranhas at different temporal and geographical scales.     

Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican <Emphasis Type="Italic">Quercus</Emphasis> (Fagaceae) species

The northern Neotropical region is characterized by a heterogeneous geological and climatic history. Recent studies have shown contrasting patterns regarding the role of geographic elements as barriers that could have determined phylogeographic structure in various species. Recently, the phylogeography and biogeography of Quercus species have been studied intensively, and the patterns observed so far suggest contrasting evolutionary histories for Neotropical species in comparison with their Holarctic relatives. The goal of this study was to describe the phylogeographic structure of two Neotropical oak species (Quercus insignis and Quercus sapotifolia) in the context of the geological and palaeoclimatic history of the northern Neotropics. Populations through the distribution range of both species were collected and characterized using nine chloroplast DNA microsatellite loci. Both oak species showed high levels of genetic diversity and strong phylogeographic structure. The distribution of genetic variation in Q. insignis suggested an influence of two major barriers, the Isthmus of Tehuantepec and the Nicaraguan Depression, while Q. sapotifolia exhibited a genetic structure defined by the heterogeneity of the Chortis highlands. The haplotype networks of both species indicated complex histories, suggesting that colonization from the Sierra Madre de Chiapas to central Mexico and from the north of the Nicaraguan Depression to the Costa Rican mountains may have occurred during different stages, and apparently more than one time. In conclusion, the phylogeographic structure of Neotropical oak species seems to be defined by a combination of geological and climatic events.     

Evolution after the flood: phylogeography of the desert fish Utah Chub

The Bonneville Basin and upper Snake River drainage of western North America underwent extensive hydrological changes during the late Pleistocene, potentially influencing the geographic distribution and evolutionary trajectories of aquatic species that occupied this region. To test this hypothesis, I reconstructed the phylogeographic history of the desert fish Utah chub (Gila atraria) by examining 16 populations that span the natural distribution of this species across the Bonneville Basin and upper Snake River. I compared mitochondrial control region sequences (934 bp) among 77 individuals revealing 24 unique haplotypes. Geographic and phylogenetic relationships among haplotypes were explored using parsimony, maximum likelihood, nested clade analysis, and analysis of molecular variance. I found that G. atraria is composed of two distinct clades that represent an early Pleistocene split between the upper Snake River and Bonneville Basin. Within each of these clades, geographic structuring was highly concordant with the hydrological history of late Pleistocene Lake Bonneville and the upper Snake River, suggesting that glacial-induced shifts in climate and unpredictable geological events have played a major role in shaping genetic subdivision among populations. To examine the effects of vicariant events on phenotypic divergence among Utah chub populations, I mapped chub life histories to the control region haplotype network. I found a nonrandom association between haplotypes and life-history phenotypes. These results suggest that historical events responsible for population fragmentation may have also contributed to phenotypic shifts in life histories, both indirectly by limiting gene flow among populations and directly by altering the selective environments where populations persisted.     

Species distribution modelling and cpSSR reveal population history of the Neotropical annual herb Tithonia rotundifolia (Asteraceae)

• The impacts of the historical geologic and climatic events on the diversity and genetic structure of Neotropical taxa have recently become a subject of study. However, annual plants associated with tropical dry forests remain under‐studied. The exploration of additional taxa in contrasting environments will improve the current understanding of responses of the Neotropical biota to these events. Here, we explore the species distribution and geographic structure of the annual herb Tithonia rotundifolia.
• We sampled 175 individuals from 19 populations of T. rotundifolia. Species distribution modelling and six microsatellite chloroplast loci were used to infer its population history. We identified areas of historical climate suitability and then tested if there is genetic structuring among these areas.
• Haplotypes showed strong phylogeographic structure. Historical climatic suitability areas were found along the Pacific coast; however, a gap was found at the Isthmus of Tehuantepec (IT). Although Bayesian analysis showed population structuring, amova revealed that the IT is not its main driver. Instead, a subdivision into a higher number of regions had higher F_CT values. Also, populations to the east of the IT showed evidence of recent population expansion and migration in a south–north direction.
• Pleistocene climate fluctuations partially explain the geographic structure of T. rotundifolia. However, life‐history characteristics such as limited seed dispersal and the patchy distribution of suitable habitats explain the high haplotype diversity and population sub‐structuring and diversity. Lastly, the absence of geographic structure of some haplotypes may indicate long‐distance dispersal, or hybridisation with the closely related T. tubaeformis.

     

Biogeographic scenarios for the diversification of a widespread Neotropical species,Glossophaga soricina (Chiroptera: Phyllostomidae)

In order to contribute to the understanding of the effect of geological and climatic changes on species diversification in the Neotropics, we employed molecular techniques to study the population dynamics of the glossophagine bat Glossophaga soricina, a widespread species in the Neotropical region. We aimed to assess the dispersal and distribution of mtDNA lineages of G. soricina and evaluate the possible effect of vicariant events in the population history and dynamics. Glossophaga soricina presented two main highly supported mtDNA lineages, which diverged between ～2.4 and 5 million years ago, probably following a vicariant event caused by the Andes final uplift. The lower sea level during Pleistocene glaciations also made possible the occupation of Jamaica after an event of dispersion over the Caribbean Sea, although past climatic fluctuations had little effect over population dynamics of G. soricina. Our results corroborate the idea that the Andes uplift played an important role in the evolution of Neotropical biodiversity. In this context we suggest that geographic events causing large scale environmental disjunction, such as the uplift of mountains, are more likely to restrict gene flow amongst populations of tolerant species with broad geographic range than local climate driven environmental changes.     

Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia

We examine the effects of historical climate change on vertebrate differentiation in tropical rainforest by comparing phylogeographic patterns in six species of widespread rainforest-restricted herpetofauna from throughout the Wet Tropics of Australia. Qualitative and quantitative comparisons of phylogeographic structure reveal strikingly similar patterns of pre-Pleistocene vicariant population differentiation on either side of a previously identified biogeographic break (variously referred to as the Black Mountain Barrier or Corridor; BMC). While divergence across the BMC antedates the Pleistocene, the impact of Quaternary climate change is apparent in populations on either side of the BMC. Consistent with palaeoclimatological reconstructions for the region, the distribution and degree of mtDNA diversity suggests that populations were fragmented and reduced to multiple refugia during Pleistocene glacial periods, with expansion following Holocene rainforest recovery. This pattern is repeated on both sides of the BMC, but substantial differences in the amount and distribution of mtDNA diversity within species indicate the importance of species-specific ecological characteristics. The historical processes of extinction and (re)colonization revealed by the comparative phylogeographic analysis of mtDNA sequences substantiate earlier suggestions that current regional patterns of species distribution and diversity in the Wet Tropics are largely determined by local extinctions and subsequent recolonization driven by Quaternary climate changes.     

Contrasting phylogeographic signatures in two Australo‐Papuan bowerbird species complexes (Aves: Ailuroedus)

The Australo‐Papuan catbird genus Ailuroedus has a complex distribution and a contested taxonomy. Here, we integrate phylogenetic analysis of DNA data and morphology to study the group's biogeography and to re‐examine its taxonomy. We couple phylogeographic and abiotic data to examine differences between the major groups defined in our phylogenetic analysis. Our results are consistent with Ailuroedus catbirds being divided into two species complexes, one distributed in humid forests in the lowlands on New Guinea and another in comparably drier and colder forests mainly in mid‐mountains on New Guinea and Australia. Vicariant events during the Pliocene are surmised to have been the major force in shaping the contemporary phylogeographical signature of this genus. Several previously suggested vicariant events, such as fragmentation of xeric forests in Australia and the uplift of the central mountain range on New Guinea, are reinforced as important Pliocene barriers for tropical forest taxa in this region. Interaction between Pleistocene climatic fluctuations and differences in habitat requirements may explain a higher and more recent population structures in the mid‐mountain catbird complex and the lack of representatives from the lowland clade in the comparably drier Australia. Phylogeographical patterns in both catbird complexes, respectively, both comply and deviate from other lowland and mid‐mountain taxa in the region. This highlights that taxon‐specific properties, such as their historical spatial and ecological distributions, capacity to disperse and tolerance to habitat changes, affect the phylogeographical histories of organisms. Within both species complexes, the genetic differentiation between several geographically isolated populations was found to exceed those commonly observed for avian sister species. As these genetically distinct taxa also were found to be morphological diagnosable, we suggest a revised classification of the genus Ailuroedus, where we recognize three species within the lowland complex and seven species within the mid‐mountain complex.     

Phylogeography of a species complex of lowland Neotropical rain forest trees (Carapa,Meliaceae)

Aim Many tropical tree species have poorly delimited taxonomic boundaries and contain undescribed or cryptic species. We examined the genetic structure of a species complex in the tree genus Carapa in the Neotropics in order to evaluate age, geographic patterns of diversity and evolutionary relationships, and to quantify levels of introgression among currently recognized species. Location Lowland moist forests in the Guiana Shield, the Central and Western Amazon Basin, Chocó and Central America. Methods Genetic structure was analysed using seven nuclear simple sequence repeats (nuSSR), five chloroplast SSRs (cpSSR), and two chloroplast DNA (cpDNA) intergenic sequences (trnH–psbA and trnC–ycf6). Bayesian clustering analysis of the SSR data was used to infer population genetic structure and to assign 324 samples to their most likely genetic cluster. Bayesian coalescence analyses were performed on the two cpDNA markers to estimate evolutionary relationships and divergence times. Results Two genetic clusters (nu_guianensis and nu_surinamensis) were detected, which correspond to the Neotropical species C. guianensis (sensu latu) and C. surinamensis. Fourteen cpDNA haplotypes clustered into six haplogroups distributed between the two nuclear genetic clusters. Divergence between the haplogroups was initiated in the Miocene, with some haplotype structure evolving as recently as the Pleistocene. The absence of complete lineage sorting between the nuclear and chloroplast genomes and the presence of hybrid individuals suggest that interspecific reproductive barriers are incomplete. NuSSR diversity was highest in C. guianensis and, within C. guianensis, cpDNA diversity was highest in the Central and Western Amazon Basin. Regional genetic differentiation was strong but did not conform to an isolation‐by‐distance process or exhibit a phylogeographical signal. Main conclusions The biogeographical history of Neotropical Carapa appears to have been influenced by events that took place during the Neogene. Our results point to an Amazonian centre of origin and diversification of Neotropical Carapa, with subsequent migration to the Pacific coast of South America and Central America. Gene flow apparently occurs among species, and introgression events are supported by inconsistencies between chloroplast and nuclear lineage sorting. The absence of phylogeographical structure may be a result of the ineffectiveness of geographical barriers among populations and of reproductive isolation mechanisms among incipient and cryptic species in this species complex.     

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.     

Range-wide phylogeography of a temperate lizard, the five-lined skink (Eumeces fasciatus)

We used mitochondrial DNA and microsatellite loci to examine the phylogeographic patterns of the most broadly distributed lizard in eastern North America, the five-lined skink (Eumeces fasciatus). We infer that longitudinal phylogeographic patterns in E. fasciatus are consistent with fragmentation due to refugial and post-glacial dynamics, but that deep divergences within the species imply historical fragmentation that predates the Pleistocene. The effect of multiple refugia is implied from our nested clade analyses, including a northern refugium in Wisconsin. Analysis of population structure using nuclear microsatellite data within the species suggests the importance of glacial dynamics in shaping more recent genetic structuring within one widely distributed lineage that ranges from the Mississippi River to the Atlantic Ocean in longitude and from southern Ontario to the Gulf of Mexico in latitude. Results shed light on the historical processes that have influenced current population structure of a temperate lizard, support the striking similarity of longitudinal phylogeographic structure across many herpetofaunal species in eastern North America, and illustrate the utility of employing multiple markers in phylogeographic studies.     

Tracing an invasion: landbridges, refugia, and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus)

Abstract Pleistocene fragmentation of the Amazonian rainforest has been hypothesized to be a major cause of Neotropical speciation and diversity. However, the role and even the reality of Pleistocene forest refugia have attracted much scepticism. In Amazonia, previous phylogeographical studies have focused mostly on organisms found in the forests themselves, and generally found speciation events to have predated the Pleistocene. However, molecular studies of open-formation taxa found both north and south of the Amazonian forests, probably because of vicariance resulting from expansion of the rainforests, may provide novel insights into the age of continuous forest cover across the Amazon basin. Here, we analyse three mitochondrial genes to infer the phylogeography of one such trans-Amazonian vicariant, the Neotropical rattlesnake (Crotalus durissus), which occupies primarily seasonal formations from Mexico to Argentina, but avoids the rainforests of Central and tropical South America. The phylogeographical pattern is consistent with gradual dispersal along the Central American Isthmus, followed by more rapid dispersal into and across South America after the uplift of the Isthmus of Panama. Low sequence divergence between populations from north and south of the Amazon rainforest is consistent with mid-Pleistocene divergence, approximately 1.1 million years ago (Ma). This suggests that the Amazonian rainforests must have become fragmented or at least shrunk considerably during that period, lending support to the Pleistocene refugia theory as an important cause of distribution patterns, if not necessarily speciation, in Amazonian forest organisms. These results highlight the potential of nonforest species to contribute to an understanding of the history of the Amazonian rainforests themselves.     

Vicariance and dispersal effects on phylogeographic structure and speciation in a widespread estuarine invertebrate

Vicariance and dispersal can strongly influence population genetic structure and allopatric speciation, but their importance in the origin of marine biodiversity is unresolved. In transitional estuarine environments, habitat discreteness and dispersal barriers could enhance divergence and provide insight to evolutionary mechanisms underlying marine and freshwater biodiversity. We examined this by assessing phylogeographic structure in the widespread amphipod Gammarus tigrinus across 13 estuaries spanning its northwest Atlantic range from Quebec to Florida. Mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 1 phylogenies supported deep genetic structure consistent with Pliocene separation and cryptic northern and southern species. This break occurred across the Virginian-Carolinian coastal biogeographic zone, where an oceanographic discontinuity may restrict gene flow. Ten estuarine populations of the northern species occurred in four distinct clades, supportive of Pleistocene separation. Glaciation effects on genetic structure of estuarine populations are largely unknown, but analysis of molecular variance (AMOVA) supported a phylogeographic break among clades in formerly glaciated versus nonglaciated areas across Cape Cod, Massachusetts. This finding was concordant with patterns in other coastal species, though there was no significant relationship between latitude and genetic diversity. This supports Pleistocene vicariance events and divergence of clades in different northern glacial refugia. AMOVA results and private haplotypes in most populations support an allopatric distribution across estuaries. Clade mixture zones are consistent with historical colonization and human-mediated transfer. An isolation-by-distance model of divergence was detected after we excluded a suspected invasive haplotype in the St. Lawrence estuary. The occurrence of cryptic species and divergent population structure support limited dispersal, dispersed habitat distribution, and historical factors as important determinants of estuarine speciation and diversification.     

In situ genetic differentiation in a Hispaniolan lizard (Ameiva chrysolaema): a multilocus perspective

A previous phylogeographic study of mitochondrial haplotypes for the Hispaniolan lizard Ameiva chrysolaema revealed deep genetic structure associated with seawater inundation during the late Pliocene/early Pleistocene and evidence of subsequent population expansion into formerly inundated areas. We revisit hypotheses generated by our previous study using increased geographic sampling of populations and analysis of three nuclear markers (alpha-enolase intron 8, alpha-cardiac-actin intron 4, and beta-actin intron 3) in addition to mitochondrial haplotypes (ND2). Large genetic discontinuities correspond spatially and temporally with historical barriers to gene flow (sea inundations). NCPA cross-validation analysis and Bayesian multilocus analyses of divergence times (IMa and MCMCcoal) reveal two separate episodes of fragmentation associated with Pliocene and Pleistocene sea inundations, separating the species into historically separate Northern, East-Central, West-Central, and Southern population lineages. Multilocus Bayesian analysis using IMa indicates asymmetrical migration from the East-Central to the West-Central populations following secondary contact, consistent with expectations from the more pervasive sea inundation in the western region. The West-Central lineage has a genetic signature of population growth consistent with the expectation of geographic expansion into formerly inundated areas. Within each lineage, significant spatial genetic structure indicates isolation by distance at comparable temporal scales. This study adds to the growing body of evidence that vicariant speciation may be the prevailing source of lineage accumulation on oceanic islands. Thus, prior theories of island biogeography generally underestimate the role and temporal scale of intra-island vicariant processes.