The aggregate site frequency spectrum for comparative population genomic inference

Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co‐distributed species for assemblage‐level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large‐scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next‐generation comparative population genomic inference.     

Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high‐throughput next‐generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341 045 sequence reads from 12 populations that we were able to assemble into 15 262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non‐model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome‐level φ_ST while appropriately modelling uncertainty in locus‐specific φ_ST. We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome‐level φ_ST were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post‐Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome‐level data to better understand the phylogeographic history of populations.     

ABC inference of multi‐population divergence with admixture from unphased population genomic data

Rapidly developing sequencing technologies and declining costs have made it possible to collect genome‐scale data from population‐level samples in nonmodel systems. Inferential tools for historical demography given these data sets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large data sets that are now attainable from nonmodel taxa through current genomic sequencing technologies. We develop and test an ABC framework for model selection and parameter estimation, given histories of three‐population divergence with admixture. We then explore different sampling regimes to illustrate how sampling more loci, longer loci or more individuals affects the quality of model selection and parameter estimation in this ABC framework. Our results show that inferences improved substantially with increases in the number and/or length of sequenced loci, while less benefit was gained by sampling large numbers of individuals. Optimal sampling strategies given our inferential models included at least 2000 loci, each approximately 2 kb in length, sampled from five diploid individuals per population, although specific strategies are model and question dependent. We tested our ABC approach through simulation‐based cross‐validations and illustrate its application using previously analysed data from the oak gall wasp, Biorhiza pallida.     

Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome‐wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans‐Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter‐riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.     

Colonization and/or mitochondrial selective sweeps across the North Atlantic intertidal assemblage revealed by multi‐taxa approximate Bayesian computation

Intertidal and subtidal communities of the western and eastern coasts of the North Atlantic Ocean were greatly affected by Pleistocene glaciations, with some taxa persisting on both coasts, and others recolonizing after being extirpated on one coast during the Last Glacial Maximum. In the original spirit of comparative phylogeography, we conducted a comparative analysis using mtDNA sequence data and a hierarchical approximate Bayesian computation (ABC) approach for testing these two scenarios across 12 intertidal and subtidal coastal invertebrates spanning the North Atlantic to determine the temporal dynamics of species membership of these two ephemeral communities. Conditioning on a low gene‐flow model, our results suggested that a colonization or mitochondrial selective sweep history was predominant across all taxa, with only the bivalve mollusc Mytilus edulis showing a history of trans‐Atlantic persistence. Conditioning on a high gene‐flow model weakened the support for this assemblage‐level demographic history. The predominance of a colonization‐type history also highlights concerns about analyses based on single‐locus data where genetic hitchhiking may be incorrectly inferred as colonization. In conclusion, driving factors in shifting species range distributions and membership of ephemeral coastal communities could be species‐specific environmental tolerances, species interactions, and/or stochastic demographic extinction. Through a re‐examination of a long‐standing question of North Atlantic phylogeography, we highlight the flexibility and statistical honesty of using a model‐based ABC approach.     

Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach

Background  

Marine allopatric speciation is an enigma because pelagic larval dispersal can potentially connect disjunct populations thereby preventing reproductive and morphological divergence. Here we present a new hierarchical approximate Bayesian computation model (HABC) that tests two hypotheses of marine allopatric speciation: 1.) "soft vicariance", where a speciation involves fragmentation of a large widespread ancestral species range that was previously connected by long distance gene flow; and 2.) peripatric colonization, where speciations in peripheral archipelagos emerge from sweepstakes colonizations from central source regions. The HABC approach analyzes all the phylogeographic datasets at once in order to make across taxon-pair inferences about biogeographic processes while explicitly allowing for uncertainty in the demographic differences within each taxon-pair. Our method uses comparative phylogeographic data that consists of single locus mtDNA sequences from multiple co-distributed taxa containing pairs of central and peripheral populations. We use the method on two comparative phylogeographic data sets consisting of cowrie gastropod endemics co-distributed in the Hawaiian (11 taxon-pairs) and Marquesan archipelagos (7 taxon-pairs).     

Sequence capture using PCR‐generated probes: a cost‐effective method of targeted high‐throughput sequencing for nonmodel organisms

Recent advances in high‐throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in‐solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR‐generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25–100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.     

The evolution of phylogeographic data sets

Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next‐generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5 years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single‐species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach ~20 000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.     

Cycles of trans‐Arctic dispersal and vicariance,and diversification of the amphi‐boreal marine fauna

The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter‐oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans‐Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter‐oceanic affinities and dispersal histories. For a general view on the trans‐Arctic dynamics and of the roles of potential dispersal–vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi‐boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter‐oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene–Pleistocene–Holocene time frame. Repeated inter‐oceanic exchange was inferred for 23 taxa, and the latest connection was usually post‐glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late‐ or post‐glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter‐oceanic vicariance scenario underlying amphi‐boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.     

Integrating broad‐scale data to assess demographic and climatic contributions to population change in a declining songbird

Climate variation and trends affect species distribution and abundance across large spatial extents. However, most studies that predict species response to climate are implemented at small spatial scales or are based on occurrence‐environment relationships that lack mechanistic detail. Here, we develop an integrated population model (IPM) for multi‐site count and capture‐recapture data for a declining migratory songbird, Wilson's warbler (Cardellina pusilla), in three genetically distinct breeding populations in western North America. We include climate covariates of vital rates, including spring temperatures on the breeding grounds, drought on the wintering range in northwest Mexico, and wind conditions during spring migration. Spring temperatures were positively related to productivity in Sierra Nevada and Pacific Northwest genetic groups, and annual changes in productivity were important predictors of changes in growth rate in these populations. Drought condition on the wintering grounds was a strong predictor of adult survival for coastal California and Sierra Nevada populations; however, adult survival played a relatively minor role in explaining annual variation in population change. A latent parameter representing a mixture of first‐year survival and immigration was the largest contributor to variation in population change; however, this parameter was estimated imprecisely, and its importance likely reflects, in part, differences in spatio‐temporal distribution of samples between count and capture‐recapture data sets. Our modeling approach represents a novel and flexible framework for linking broad‐scale multi‐site monitoring data sets. Our results highlight both the potential of the approach for extension to additional species and systems, as well as needs for additional data and/or model development.     

HTAPP: High‐throughput autonomous proteomic pipeline

Recent advances in the speed and sensitivity of mass spectrometers and in analytical methods, the exponential acceleration of computer processing speeds, and the availability of genomic databases from an array of species and protein information databases have led to a deluge of proteomic data. The development of a lab‐based automated proteomic software platform for the automated collection, processing, storage, and visualization of expansive proteomic data sets is critically important. The high‐throughput autonomous proteomic pipeline described here is designed from the ground up to provide critically important flexibility for diverse proteomic workflows and to streamline the total analysis of a complex proteomic sample. This tool is composed of a software that controls the acquisition of mass spectral data along with automation of post‐acquisition tasks such as peptide quantification, clustered MS/MS spectral database searching, statistical validation, and data exploration within a user‐configurable lab‐based relational database. The software design of high‐throughput autonomous proteomic pipeline focuses on accommodating diverse workflows and providing missing software functionality to a wide range of proteomic researchers to accelerate the extraction of biological meaning from immense proteomic data sets. Although individual software modules in our integrated technology platform may have some similarities to existing tools, the true novelty of the approach described here is in the synergistic and flexible combination of these tools to provide an integrated and efficient analysis of proteomic samples.     

Reductions in complexity of mitochondrial genomes in lichen‐forming fungi shed light on genome architecture of obligate symbioses

Symbioses among co‐evolving taxa are often marked by genome reductions such as a loss of protein‐coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under‐studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and annotated species of lichenized fungi were compared to 167 mitochondrial genomes of nonlichenized fungi. Our results demonstrate the first broad‐scale loss of atp9 from mitochondria of lichenized fungi. Despite key functions in mitochondrial energy production, we show that atp9 has been independently lost in three different lineages spanning 10 of the 22 studied species. A search for predicted, functional copies of atp9 among genomes of other symbionts involved in each lichen revealed the full‐length, presumably functional copies of atp9 in either the photosynthetic algal partner or in other symbiotic fungi in all 10 instances. Together, these data yield evidence of an obligate symbiotic relationship in which core genomic processes have been streamlined, likely due to co‐evolution.     

Phylogeography and population genetics of the maize stalk borer Busseola fusca (Lepidoptera, Noctuidae) in sub-Saharan Africa

The population genetics and phylogeography of African phytophagous insects have received little attention. Some, such as the maize stalk borer Busseola fusca, display significant geographic differences in ecological preferences that may be congruent with patterns of molecular variation. To test this, we collected 307 individuals of this species from maize and cultivated sorghum at 52 localities in West, Central and East Africa during the growing season. For all collected individuals, we sequenced a fragment of the mitochondrial cytochrome b. We tested hypotheses concerning the history and demographic structure of this species. Phylogenetic analyses and nested clade phylogeographic analyses (NCPA) separated the populations into three mitochondrial clades, one from West Africa, and two--Kenya I and Kenya II--from East and Central Africa. The similar nucleotide divergence between clades and nucleotide diversity within clades suggest that they became isolated at about the same time in three different refuges in sub-Saharan Africa and have similar demographic histories. The results of mismatch distribution analyses were consistent with the demographic expansion of these clades. Analysis of molecular variance (amova) indicated a high level of geographic differentiation at different hierarchical levels. NCPA suggested that the observed distribution of haplotypes at several hierarchical levels within the three major clades is best accounted for by restricted gene flow with isolation by distance. The domestication of sorghum and the introduction of maize in Africa had no visible effect on the geographic patterns observed in the B. fusca mitochondrial genome.     

Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait‐based phylogeographic approach

Hypotheses to explain phylogeographic structure traditionally invoke geographic features, but often fail to provide a general explanation for spatial patterns of genetic variation. Organisms' intrinsic characteristics might play more important roles than landscape features in determining phylogeographic structure. We developed a novel comparative approach to explore the role of ecological and life‐history variables in determining spatial genetic variation and tested it on frog communities in Panama. We quantified spatial genetic variation within 31 anuran species based on mitochondrial DNA sequences, for which hierarchical approximate Bayesian computation analyses rejected simultaneous divergence over a common landscape. Regressing ecological variables, on genetic divergence allowed us to test the importance of individual variables revealing that body size, current landscape resistance, geographic range, biogeographic origin and reproductive mode were significant predictors of spatial genetic variation. Our results support the idea that phylogeographic structure represents the outcome of an interaction between organisms and their environment, and suggest a conceptual integration we refer to as trait‐based phylogeography.     

A striking lack of genetic diversity across the wide-ranging amphibian <Emphasis Type="Italic">Gastrophryne carolinensis</Emphasis> (Anura: Microhylidae)

We examine phylogeographic structure across a wide-ranging microhylid frog (Gastrophryne carolinensis) using both mitochondrial (mtDNA) and nuclear (AFLP) data. Species with similar ecological characteristics such as large range size, low vagility, or existence across known biogeographic barriers, often are comprised of multiple, cryptic lineages. Surprisingly, our analyses of both portions of the genome show very little phylogeographic or population genetic structure. The family Microhylidae is one of the largest families of anurans with over 60 genera and around 400 species distributed across much of the world (Americas, Asia, Africa, and Madagascar), but very few phylogeographic studies have assessed intraspecific genetic diversity across the mitochondrial and nuclear genomes. Our results suggest that G. carolinensis, one of only three species of microhylid native to the US, has experienced a severe population bottleneck with subsequent range expansion. Comparable molecular data from closely related microhylids, in addition to demographic and ecological analyses, will provide valuable insight into patterns of genetic diversity and the processes driving phylogeographic diversity in these wide-ranging frogs.     

Cryptic species and co‐diversification in sand scorpions from the Karakum and Kyzylkum deserts of Central Asia

Little is known about species diversification within the deserts of Central Asia. For example, the degree of lineage divergence and timing of population differentiation, as well as potential biogeographic barriers driving diversification, are nearly unknown. Here, we analysed a multi‐locus data set for a widespread sand scorpion (Mesobuthus gorelovi) to evaluate cryptic species diversity and phylogeographic patterns across the Karakum and Kyzylkum deserts. We also combined these data with previously published sequence data to test for a signal of co‐diversification. A consensus species delimitation approach indicated that the widespread M. gorelovi is likely composed of up to five distinct species that began to diversify at the Miocene–Pliocene boundary. We observed shared patterns of lineage divergence across the Amu Darya River region in three scorpion taxa and found support for a shared history of assemblage diversification across this biogeographic barrier. Thus, major river systems appear to facilitate diversification among desert scorpions.     

Phylogeography at large spatial scales: incongruent patterns of population structure and demography of Pan‐American butterflies associated with weedy habitats

Aim Few studies of comparative phylogeography have been conducted at very large spatial scales, encompassing species that are distributed across multiple continents. Several Pan‐American butterfly species associated with weedy, human‐modified habitats were studied using comparative phylogeographic tools to test for the congruence of demographic histories across a range of spatial scales and to investigate the effects of human‐facilitated range expansion. Location North and South America, mainly the southern United States, Brazil and Argentina. Methods The mitochondrial DNA cytochrome c oxidase subunit II region (COII) was sequenced for Hylephila phyleus, Lerodea eufala, Erynnis funeralis and Agraulis vanillae across their North and South American ranges. Data from these conspecifics were compared with variation in COII sequences between allopatric congener pairs on both continents whose ranges approximate the conspecifics and also share similar weedy habitat associations: Ancyloxypha numitor versus Ancyloxypha nitedula, Vanessa annabella versus Vanessa carye, and Euptoieta claudia versus Euptoieta hortensia. We tested for similarities in demographic histories within and across continents for each species using pairwise distances, population genetic statistics, mismatch distributions and deviations from mutation‐drift equilibrium. Results Mean pairwise divergence across continents was lower for Lerodea eufala and Hylephila phyleus (with several shared Pan‐American haplotypes each) compared with Erynnis funeralis and Agraulis vanillae (both with no shared haplotypes). Differentiation between congeneric species pairs was generally significantly higher than conspecific divergence across continents, but North and South American populations of A. vanillae were more divergent than V. annabella and V. carye. We found deviations from mutation‐drift equilibrium in A. vanillae. Population‐level variation was greater than the variation across continents for H. phyleus and L. eufala. Main conclusions We find little congruence in phylogeographic patterns among these taxa across continents, although similar demographic patterns can be detected at smaller regional levels. Except for Californian populations of some species, the North American distributions of these weedy butterfly species appear to largely pre‐date the influences of human‐facilitated range expansion.     

Next‐Gen phylogeography of rainforest trees: exploring landscape‐level cpDNA variation from whole‐genome sequencing

Standardized phylogeographic studies across codistributed taxa can identify important refugia and biogeographic barriers, and potentially uncover how changes in adaptive constraints through space and time impact on the distribution of genetic diversity. The combination of next‐generation sequencing and methodologies that enable uncomplicated analysis of the full chloroplast genome may provide an invaluable resource for such studies. Here, we assess the potential of a shotgun‐based method across twelve nonmodel rainforest trees sampled from two evolutionary distinct regions. Whole genomic shotgun sequencing libraries consisting of pooled individuals were used to assemble species‐specific chloroplast references (in silicio). For each species, the pooled libraries allowed for the detection of variation within and between data sets (each representing a geographic region). The potential use of nuclear rDNA as an additional marker from the NGS libraries was investigated by mapping reads against available references. We successfully obtained phylogeographically informative sequence data from a range of previously unstudied rainforest trees. Greater levels of diversity were found in northern refugial rainforests than in southern expansion areas. The genetic signatures of varying evolutionary histories were detected, and interesting associative patterns between functional characteristics and genetic diversity were identified. This approach can suit a wide range of landscape‐level studies. As the key laboratory‐based steps do not require prior species‐specific knowledge and can be easily outsourced, the techniques described here are even suitable for researchers without access to wet‐laboratory facilities, making evolutionary ecology questions increasingly accessible to the research community.     

Targeted multiplex next‐generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

Next‐generation sequencing (NGS) is emerging as an efficient and cost‐effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi‐genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of DNA sequence from one species to capture and enrich the sequencing libraries of another species (i.e. cross‐species DNA capture) indicates that efficient enrichment occurs when sequences are up to about 12% divergent, allowing us to take advantage of genomic information in one species to sequence orthologous regions in related species. In addition to a complete mitochondrial genome on each array, we have included between 43 and 118 nuclear loci for low‐coverage sequencing of between 18 kb and 87 kb of DNA sequence per individual for single nucleotide polymorphisms discovery from 50 to 100 individuals in a single sequencing lane. Using this method, we have generated a total of over 500 whole mitochondrial genomes from seven cetacean species and green sea turtles. The greater variation detected in mitogenomes relative to short mtDNA sequences is helping to resolve genetic structure ranging from geographic to species‐level differences. These NGS and analysis techniques have allowed for simultaneous population genomic studies of mtDNA and nDNA with greater genomic coverage and phylogeographic resolution than has previously been possible in marine mammals and turtles.     

The odd couple: contrasting phylogeographic patterns in two sympatric sibling species of woodlouse‐hunter spiders in the Canary Islands

Comparative phylogeography seeks for commonalities in the spatial demographic history of sympatric organisms to characterize the mechanisms that shaped such patterns. The unveiling of incongruent phylogeographic patterns in co‐occurring species, on the other hand, may hint to overlooked differences in their life histories or microhabitat preferences. The woodlouse‐hunter spiders of the genus Dysdera have undergone a major diversification on the Canary Islands. The species pair Dysdera alegranzaensis and Dysdera nesiotes are endemic to the island of Lanzarote and nearby islets, where they co‐occur at most of their known localities. The two species stand in sharp contrast to other sympatric endemic Dysdera in showing no evidence of somatic (non‐genitalic) differentiation. Phylogenetic and population genetic analyses of mitochondrial cox1 sequences from an exhaustive sample of D. alegranzaensis and D. nesiotes specimens, and additional mitochondrial (16S, L1, nad1) and nuclear genes (28S, H3) were analysed to reveal their phylogeographic patterns and clarify their phylogenetic relationships. Relaxed molecular clock models using five calibration points were further used to estimate divergence times between species and populations. Striking differences in phylogeography and population structure between the two species were observed. Dysdera nesiotes displayed a metapopulation‐like structure, while D. alegranzaensis was characterized by a weaker geographical structure but greater genetic divergences among its main haplotype lineages, suggesting more complex population dynamics. Our study confirms that co‐distributed sibling species may exhibit contrasting phylogeographic patterns in the absence of somatic differentiation. Further ecological studies, however, will be necessary to clarify whether the contrasting phylogeographies may hint at an overlooked niche partitioning between the two species. In addition, further comparisons with available phylogeographic data of other eastern Canarian Dysdera endemics confirm the key role of lava flows in structuring local populations in oceanic islands and identify localities that acted as refugia during volcanic eruptions.