THE AUTOMATION AND EVALUATION OF NESTED CLADE PHYLOGEOGRAPHIC ANALYSIS

The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics

Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.

"Colonization routes and demographic history of Chirostoma humboldtianum in the central Mexican plateau"

In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico.

First glimpse into the origin and spread of the Asian longhorned tick, Haemaphysalis longicornis, in the United States

Established populations of Asian longhorned ticks (ALT), Haemaphysalis longicornis, were first identified in the United States (US) in 2017 by sequencing the mitochondrial cytochrome c oxidase subunit I (cox1) 'barcoding' locus followed by morphological confirmation. Subsequent investigations detected ALT infestations in 12, mostly eastern, US states. To gain information on the origin and spread of US ALT, we (1) sequenced cox1 from ALT populations across 9 US states and (2) obtained cox1 sequences from potential source populations [China, Japan and Republic of Korea (ROK) as well as Australia, New Zealand and the Kingdom of Tonga (KOT)] both by sequencing and by downloading publicly available sequences in NCBI GenBank. Additionally, we conducted epidemiological investigations of properties near its initial detection locale in Hunterdon County, NJ, as well as a broader risk analysis for importation of ectoparasites into the area. In eastern Asian populations (China/Japan/ROK), we detected 35 cox1 haplotypes that neatly clustered into two clades with known bisexual versus parthenogenetic phenotypes. In Australia/New Zealand/KOT, we detected 10 cox1 haplotypes all falling within the parthenogenetic cluster. In the United States, we detected three differentially distributed cox1 haplotypes from the parthenogenetic cluster, supporting phenotypic evidence that US ALT are parthenogenetic. While none of the source populations examined had all three US cox1 haplotypes, a phylogeographic network analysis supports a northeast Asian source for the US populations. Within the United States, epidemiological investigations indicate ALT can be moved long distances by human transport of animals, such as horses and dogs, with smaller scale movements on wildlife. These results have relevant implications for efforts aimed at minimizing the spread of ALT in the United States and preventing additional exotic tick introductions.

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.

Biogeographic patterns provide insight into the evolutionary and ecological processes that govern biodiversity. However, the evolutionary and ecological processes that govern terrestrial microbial diversity remain poorly characterized. We evaluated the biogeography of the genus Streptomyces to show that the diversity of terrestrial bacteria is governed by many of the same processes that govern the diversity of many plant and animal species. While bacteria of the genus Streptomyces are a preeminent source of antibiotics, their evolutionary history, biogeography, and biodiversity remain poorly characterized. The observations we describe provide insight into the drivers of Streptomyces biodiversity and the processes that underlie microbial diversification in terrestrial habitats.

Integrative analysis of DNA phylogeography and morphology of the European rose chafer (Cetonia aurata) to infer species taxonomy and patterns of postglacial colonisation in Europe

Integrative taxonomy has been proposed as a framework to unify new conceptual and methodological developments in quantitative assessment of trait variation used in species delimitation, but empirical studies in this young branch of systematics are rare. Here we use standard phylogenetic and parsimony network analyses on nuclear and mitochondrial DNA (Cox1, ITS1) of 230 individuals from 65 European sampling sites in order to deduce population structure of Cetonia beetles from geno- and haplotypes. Statistical measures of population differentiation are inferred on genealogical and geographical scales to test hypotheses about species limits and population history. By combining results of phylogenetic structure with features of morphology, including genital shape morphometrics and discrete external body characters, as well as with measures of population genetics, we attempt to integrate the results as a test of the validity of species limits, in particular of currently recognised subspecies. Despite high Cox1 divergence between some haplotype lineages, even some sympatric lineages (9%, e.g. N2 vs. N4), nDNA and morphology, as well as pattern of geographical and genealogical divergence measured by AMOVA analysis did not support the hypothesis of separate species. Highest divergence in nuclear markers was found among Italian populations of C. aurata pisana and C. a. sicula, and moderately high fixation indices along measurable morphological divergence suggest the correctness of their status as 'subspecies'. Divergence time estimates of the lineages suggest a glacial divergence in different refugia between the major haplogroups, while population differentiation in mtDNA among these was primarily attributable to restricted gene flow caused by geographic isolation.

Phylogeography of the ant Myrmica rubra and its inquiline social parasite

Widely distributed Palearctic insects are ideal to study phylogeographic patterns owing to their high potential to survive in many Pleistocene refugia and—after the glaciation—to recolonize vast, continuous areas. Nevertheless, such species have received little phylogeographic attention. Here, we investigated the Pleistocene refugia and subsequent postglacial colonization of the common, abundant, and widely distributed ant Myrmica rubra over most of its Palearctic area, using mitochondrial DNA (mtDNA). The western and eastern populations of M. rubra belonged predominantly to separate haplogroups, which formed a broad secondary contact zone in Central Europe. The distribution of genetic diversity and haplogroups implied that M. rubra survived the last glaciation in multiple refugia located over an extensive area from Iberia in the west to Siberia in the east, and colonized its present areas of distribution along several routes. The matrilineal genetic structure of M. rubra was probably formed during the last glaciation and subsequent postglacial expansion. Additionally, because M. rubra has two queen morphs, the obligately socially parasitic microgyne and its macrogyne host, we tested the suggested speciation of the parasite. Locally, the parasite and host usually belonged to the same haplogroup but differed in haplotype frequencies. This indicates that genetic differentiation between the morphs is a universal pattern and thus incipient, sympatric speciation of the parasite from its host is possible. If speciation is taking place, however, it is not yet visible as lineage sorting of the mtDNA between the morphs.

Phylogeny and biogeography of the Anderson's crocodile newt, Echinotriton andersoni (Amphibia: Caudata), as revealed by mitochondrial DNA sequences

The Anderson's crocodile newt, Echinotriton andersoni, is considered a relic and endangered species distributed in the Central Ryukyus. To elucidate phylogenetic relationships and detailed genetic structures among populations, we analyzed variation in the mitochondrial cytochrome b gene. Results strongly support a primary dichotomy between populations from the Amami and Okinawa Island Groups with substantial genetic divergence, favoring a primary divergence between the two island groups. Within the latter, populations from the southern part of Okinawajima Island are shown to be more closely related to those from Tokashikijima Island than to those from the northern and central parts of Okinawajima. The prominent genetic divergence between the two island groups of the Central Ryukyus seems to have initiated in the Miocene, i.e., prior to formation of the strait that has consistently separated these island groups since the Pleistocene. The ancestor of the southern Okinawajima-Tokashikijima is estimated to have migrated from the northern and central parts of Okinawajima into southern Okinawajima at the Pleistocene, and dispersed into Tokashikijima subsequently.

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

Background

As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species.

Results

Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (G_ST = 0.988; N_ST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (G_ST = 0.222; N_ST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (N_ST > G_ST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species.

Conclusions

We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

Population genetic structure of sexual and parthenogenetic damselflies inferred from mitochondrial and nuclear markers

It has been postulated that obligate asexual lineages may persist in the long term if they escape from negative interactions with either sexual lineages or biological enemies; and thus, parthenogenetic populations will be more likely to occur in places that are difficult for sexuals to colonize, or those in which biological interactions are rare, such as islands or island-like habitats. Ischnura hastata is the only known example of natural parthenogenesis within the insect order Odonata, and it represents also a typical example of geographic parthenogenesis, as sexual populations are widely distributed in North America, whereas parthenogenetic populations of this species have only been found at the Azores archipelago. In order to gain insight in the origin and distribution of parthenogenetic I. hastata lineages, we have used microsatellites, mitochondrial and nuclear DNA sequence data, to examine the population genetic structure of this species over a wide geographic area. Our results suggest that sexual populations of I. hastata in North America conform to a large subdivided population that has gone through a recent spatial expansion. A recent single long distance dispersal event, followed by a demographic expansion, is the most parsimonious hypothesis explaining the origin of the parthenogenetic population of this species in the Azores islands.

Approximate Bayesian computation reveals the factors that influence genetic diversity and population structure of foxsnakes

Contemporary geographical range and patterns of genetic diversity within species reflect complex interactions between multiple factors acting across spatial and temporal scales, and it is notoriously difficult to disentangle causation. Here, we quantify patterns of genetic diversity and genetic population structure using mitochondrial DNA sequences (101 individuals, cytochrome b) and microsatellites (816 individuals, 12 loci) and use Approximate Bayesian computation methods to test competing models of the demographic history of eastern and western foxsnakes. Our analyses indicate that post-glacial colonization and past population declines, probably caused by the infilling of deciduous forest and cooler temperatures since the mid-Holocene, largely underpin large-scale genetic patterns for foxsnakes. At finer geographical scales, our results point to more recent anthropogenic habitat loss as having accentuated genetic population structure by causing further declines and fragmentation.

The limits of cryptic diversity in groundwater: phylogeography of the cave shrimp Troglocaris anophthalmus (Crustacea: Decapoda: Atyidae)

Recent studies have revealed high local diversity and endemism in groundwaters, and showed that species with large ranges are extremely rare. One of such species is the cave shrimp Troglocaris anophthalmus from the Dinaric Karst on the western Balkan Peninsula, apparently uniform across a range of more than 500 kilometers. As such it contradicts the paradigm that subterranean organisms form localized, long-term stable populations that cannot disperse over long distances. We tested it for possible cryptic diversity and/or unexpected evolutionary processes, analysing mitochondrial (COI, 16S rRNA) and nuclear (ITS2) genes of 232 specimens from the entire range. The results of an array of phylogeographical procedures congruently suggested that the picture of a widespread, continuously distributed and homogenous T. anophthalmus was wrong. The taxon is composed of four or possibly five monophyletic, geographically defined phylogroups that meet several species delimitation criteria, two of them showing evidence of biological reproductive isolation in sympatry. COI genetic distances between phylogroups turned out to be a poor predictor, as they were much lower than the sometimes suggested crustacean threshold value of 0.16 substitutions per site. Most results confirmed the nondispersal hypothesis of subterranean fauna, but the southern Adriatic phylogroup displayed a paradoxical pattern of recent dispersal across 300 kilometers of hydrographically fragmented karst terrain. We suggest a model of migration under extreme water-level conditions, when flooded poljes could act as stepping-stones. In the north of the range (Slovenia), the results confirmed the existence of a zone of unique biogeographical conflict, where surface fauna is concordant with the current watershed, and subterranean fauna is not.

DIM SUM: demography and individual migration simulated using a Markov chain

An increasing number of studies seek to infer demographic history, often jointly with genetic relationships. Despite numerous analytical methods for such data, few simulations have investigated the methods' power and robustness, especially when underlying assumptions have been violated. DIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration while recording ancestor-descendant relationships. It does not employ coalescent assumptions or discrete population boundaries. It is extremely flexible, allowing the user to specify border positions, reactions of organisms to borders, local and global carrying capacities, individual dispersal kernels, rates of reproduction and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from gis software) and may vary through time. In combination with software for genetic marker simulation, DIM SUM will be useful for testing phylogeographic (e.g., nested clade phylogeographic analysis, coalescent-based tests and continuous-landscape frameworks) and landscape-genetic methods, specifically regarding violations of coalescent assumptions. It can also be used to explore the qualitative features of proposed demographic scenarios (e.g. regarding biological invasions) and as a pedagogical tool. DIM SUM (with user's manual) can be downloaded from http://code.google.com/p/bio-dimsum.

A new model for extinction and recolonization in two dimensions: quantifying phylogeography

Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.

Ginkgo: spatially-explicit simulator of complex phylogeographic histories

We present Ginkgo, a software package for agent-based, forward-time simulations of genealogies of multiple unlinked loci from diploid populations. Ginkgo simulates the evolution of one or more species on a spatially explicit landscape of cells. The user of the software can specify the geographical and environmental characteristics of the landscape, and these properties can change according to a prespecified schedule. The geographical elements modelled include the arrangement of cells and movement rates between particular cells. Each species has a function that can calculate a fitness score for any combination of an individual organism's phenotype and environmental characteristics. The user can control the number of fitness factors (the dimensionality of the cell-specific fitness factors and the individuals phenotypic vectors) and the weighting of each of these dimensions in the fitness calculation. Cell-specific fitness trait optima can be specified across the landscape to mimic differences in habitat. In addition to their differing fitness functions, species can differ in terms of their vagility and fecundity. Genealogies and occurrence data can be produced at any time during the simulation in NEXUS and ESRI Ascii Grid formats, respectively.

Three roads diverged? Routes to phylogeographic inference

Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution.

Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations

BACKGROUND

Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons.

METHODOLOGY/PRINCIPAL FINDINGS

We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events.

CONCLUSIONS/SIGNIFICANCE

We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes.

A likelihood framework for estimating phylogeographic history on a continuous landscape

Due to lack of an adequate statistical framework, biologists studying phylogeography are abandoning traditional methods of estimating phylogeographic history in favor of statistical methods designed to test a priori hypotheses. These new methods may, however, have limited descriptive utility. Here, we develop a new statistical framework that can be used to both test a priori hypotheses and estimate phylogeographic history of a gene (and the statistical confidence in that history) in the absence of such hypotheses. The statistical approach concentrates on estimation of geographic locations of the ancestors of a set of sampled organisms. Now we use (2) to derive the likelihood of the ancestral geographic coordinates and the value of the scaled dispersal parameter, given the observed geographic coordinates (assuming known topology and branch lengths). Using a maximum likelihood approach, which is implemented in the new program PhyloMapper, we apply this statistical framework to a 246-taxon mitochondrial genealogy of North American chorus frogs, focusing in detail on one of these species. We demonstrate three lines of evidence for recent northward expansion of the mitochondrion of the coastal clade of Pseudacris feriarum: higher per-generation dispersal distance in the recently colonized region, a noncentral ancestral location, and directional migration. After illustrating one method of accommodating phylogenetic uncertainty, we conclude by discussing how extensions of this framework could function to incorporate a priori ecological and geological information into phylogeographic analyses.

Population genetic structure and phylogeography of masu salmon (Oncorhynchus masou masou) inferred from mitochondrial and microsatellite DNA analyses

The population genetic structure and phylogeography of masu salmon were investigated by using variation in the mitochondrial NADH dehydrogenase subunit 5 gene (ND5) and six polymorphic microsatellite loci among a total of 895 fish representing 18 populations collected from Japan (9), Russia (7), and Korea (2) from 2000 to 2008. An analysis of ND5 nucleotide sequences revealed 22 variable sites in about 560 bp in the 5' half of the gene, which defined 20 haplotypes, including some associated with geographical regions. Haplotype and nucleotide diversities were greater in the populations in Japan and Korea than in those in Russia, indicating greater genetic diversity in the Japanese and Korean populations than in the Russian populations. All the microsatellite loci examined showed a high level of variation, but the expected heterozygosity indicated a similar level of genetic diversity among the populations of the three regions, contrary to the results for ND5. However, AMOVA and pairwise population F (ST) estimates for both ND5 and the microsatellite markers indicated a similar pattern of moderate genetic differentiation among populations of the three regions, and large population groups on the coasts of the Sea of Japan, Sea of Okhotsk, and Pacific Ocean in the Far East. From a mismatch distribution analysis and neutrality test, the observed genetic structure appears to have been influenced primarily by bottlenecks during glacial periods and population expansions during interglacial periods in the late Pleistocene.

Mitochondrial DNA variation in the malaria vector Anopheles minimus across China, Thailand and Vietnam: evolutionary hypothesis, population structure and population history

The effects of Pleistocene environmental fluctuations on the distribution and diversity of organisms in Southeast Asia are much less well known than in Europe and North America. In these regions, the combination of palaeoenvironmental reconstruction and inferences about population history from genetic data has been very powerful. In Southeast Asia, mosquitoes are good candidates for the genetic approach, with the added benefit that understanding the relative contributions of historical and current processes to population structure can inform management of vector species. Genetic variation among populations of Anopheles minimus was examined using 144 mtDNA COII sequences from 23 sites in China, Thailand and Vietnam. Haplotype diversity was high, with two distinct lineages that have a sequence divergence of over 2% and exhibit different geographical distributions. We compare alternative hypotheses concerning the origin of this pattern. The observed data deviate from the expectations based on a single-panmictic population with or without growth, or a stable but spatially structured population. However, they can be readily accommodated by a model of past fragmentation into eastern and western refugia, followed by growth and range expansion. This is consistent with the palaeoenvironmental reconstructions currently available for the region.

Evaluating nested clade phylogeographic analysis under models of restricted gene flow

Nested clade phylogeographic analysis (NCPA) is a widely used method that aims to identify past demographic events that have shaped the history of a population. In an earlier study, NCPA has been fully automated, allowing it to be tested with simulated data sets generated under a null model in which samples simulated from a panmictic population are geographically distributed. It was noted that NCPA was prone to inferring false positives, corroborating earlier findings. The present study aims to evaluate both single-locus and multilocus NCPA under the scenario of restricted gene flow among spatially distributed populations. We have developed a new program, ANeCA-ML, which implements multilocus NCPA. Data were simulated under 3 models of gene flow: a stepping stone model, an island model, and a stepping stone model with some long-distance dispersal. Results indicate that single-locus NCPA tends to give a high frequency of false positives, but, unlike the random-mating scenario presented previously, inferences are not limited to restricted gene flow with isolation by distance or contiguous range expansion. The proportion of single-locus data sets that contained false inferences was 76% for the panmictic case, 87% for the stepping stone model, 79% for the stepping stone model with long-distance dispersal, and more than 99% for the island model. The frequency of inferences is inversely related to the amount of gene flow between demes. We performed multilocus NCPA by grouping the simulated loci into data sets of 5 loci. The false-positive rate was reduced in multilocus NCPA for some inferences but remained high for others. The proportion of multilocus data sets that contained false inferences was 17% for the panmictic case, 30% for the stepping stone model, 4% for the stepping stone model with long-distance dispersal, and 54% for the island model. Multilocus NCPA reduces the false-positive rate by restricting the sensitivity of the method but does not appear to increase the accuracy of the approach. Three classical tests-the analysis of molecular variance method, Fu's Fs, and the Mantel test-show that there is information in the data that gives rise to explicable results using these standard approaches. In conclusion, for the scenarios that we have examined, our simulation study suggests that the NCPA method is unreliable and its inferences may be misleading. We suggest that the NCPA method should not be used without objective simulation-based testing by independent researchers.

Phylogeography of two moray eels indicates high dispersal throughout the indo-pacific

Reef fishes disperse primarily as oceanic "pelagic" larvae, and debate continues over the extent of this dispersal, with recent evidence for geographically restricted (closed) populations in some species. In contrast, moray eels have the longest pelagic larval stages among reef fishes, possibly providing opportunities to disperse over great distances. We test this prediction by measuring mitochondrial DNA (mtDNA) and nuclear DNA variation in 2 species of moray eels, Gymnothorax undulatus (N = 165) and G. flavimarginatus (N = 124), sampled at 14-15 locations across the Indo-Pacific. The mtDNA data comprise 632 bp of cytochrome b and 596 bp of cytochrome oxidase I. Nuclear markers include 2 recombination-activating loci (421 bp of RAG-1 and 754 bp of RAG-2). Analyses of molecular variance and Mantel tests indicate little or no genetic differentiation, and no isolation by distance, across 22 000 km of the Indo-Pacific. We estimate that mitochondrial genetic variation coalesces within the past about 2.3 million years (My) for G. flavimarginatus and within the past about 5.9 My for G. undulatus. Permutation tests of geographic distance on the mitochondrial haplotype networks indicate recent range expansions for some younger haplotypes (estimated within approximately 600 000 years) and episodic fragmentation of populations at times of low sea level. Our results support the predictions that the extended larval durations of moray eels enable ocean-wide genetic continuity of populations. This is the first phylogeographic survey of the moray eels, and morays are the first reef fishes known to be genetically homogeneous across the entire Indo-Pacific.

Do Mediterranean crickets Gryllus bimaculatus De Geer (Orthoptera: Gryllidae) come from the Mediterranean? Largescale phylogeography and regional gene flow

We investigate the degree of between-population genetic differentiation in the Mediterranean field cricket Gryllus bimaculatus, as well as the possible causes of such differentiation. Using cytochrome b mtDNA sequences, we estimate genetic variation in G. bimaculatus from seven South African and two Mediterranean populations. Within-population genetic variation in Europe (two haplotypes, one unique to a single individual) suggest low effective population size and strong bottlenecks with associated founder effects, probably due to cold winter environments in Europe that limit reproduction to a short part of the summer. The likely cause for this is the daily maxima in winter temperatures that fall below the critical level of 16 degrees C (enabling normal calling and courtship behaviour) in Mediterranean Europe, whereas the equivalent temperatures in southern Africa are above this limit and enable reproduction over a large part of the year. European genetic variants were either shared with Africa or closely related to African haplotypes. For survival, European populations are probably dependent on immigration from other areas, including Africa. South African populations have low but measurable gene flow with Europe and show significant between-population genetic differentiation (30 haplotypes). Isolation-by-distance is not sufficient to explain the degree of between-population genetic differences observed, and a large degree of dispersal is also required in order to account for the observed patterns. Differences in morphology and calling behaviour among these populations are underlied by these genetic differences.

In defence of model-based inference in phylogeography

Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

Phylogeography of Phrynocephalus erythrurus from the Qiangtang Plateau of the Tibetan Plateau

Phrynocephalus erythrurus of the Qiangtang Plateau occupies the highest regions of any reptile on earth. Here, we report mitochondrial DNA haplotypes sampled throughout the distribution of P. erythrurus and analyze patterns of genetic divergence among populations. The species diverged into two major lineages/subspecies at 3.67mya corresponding to the Northern and Southern Qiangtang Plateau. The Northern Qiangtang lineage diverged into two subpopulations at 2.76mya separated by the Beilu River Region and Wulanwula Mountains. Haplotypes from the southern Qiangtang lineage diverged 0.98mya as a star-shaped pattern. Analyses of molecular variance indicated that most of the observed genetic variation occurred among populations/regions implying long-term interruptions to gene flow. There was no evidence of sudden recent range expansions within any of the clades/lineages. NCPA infers allopatric fragmentation and restricted gene flow as the most likely mechanisms of population differentiation. Our results also indicate the presence of at least three refugia since the Hongya glaciation. Mountain movement and glaciations since mid-Pliocene are considered to have shaped phylogenetic patterns of P. erythrurus. P. erythrurus parva is suggested as a valid subspecies of P. erythrurus. Using four calibration points, we estimate an evolutionary rate of 0.762% divergence per lineage per million years for a mitochondrial genomic segment comprising the genes encoding ND2, tRNA(Trp) and tRNA(Ala).