Metabolic adaptations for isopod specialization in three species of Dysdera spiders from the Canary Islands

The spider genus Dysdera is considered to comprise specialist isopod feeders, although the degree of specialization varies between species, depending on morphological (shape of chelicerae), behavioural (attack tactics) and metabolic (food quality of prey) adaptations. Dysdera has radiated extensively in the Canary Islands (currently 47 endemic species are described) and codistributed species have different cheliceral shapes and body sizes indicating different feeding niches. In the present study, we investigate the existence of metabolic adaptations to feeding on isopods by three endemic species (Dysdera insulana Simon, Dysdera macra Simon and Dysdera verneaui Simon) from Tenerife. We hypothesize that there is enhanced extraction efficiency of fundamental macronutrients from isopods compared with control prey in species with special morphological and behavioural adaptations for this prey type. We measure quantitatively spider growth, dry mass consumption, lipid and nitrogen consumption, and calculate growth efficiency and efficiency of utilization of dry mass, lipid and nitrogen. The results show that all three species are able to utilize both prey types, indicating that none of them are strict isopod specialist. Dysdera insulana shows enhanced growth efficiency and D. macra shows enhanced nitrogen extraction efficiency compared with D. verneaui when feeding on Porcellio rather than on Musca. Both traits indicate likely adaptations for the utilization of isopods. Spider species, sex and prey type all affect lipid and nitrogen extraction efficiencies, indicating that spiders do not simply extract nutrients in the proportions available. The results support the hypothesis that adaptations for enhanced digestion of focal prey evolve in species that already have adaptations for enhanced capture success.     

Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa's Great Lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non‐cichlid littoral taxa from these systems. To begin to address this, we generated restriction‐site‐associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika (LT) in two broadly sympatric rocky shore catfish species from independent evolutionary radiations with differing behaviors: the mouthbrooding claroteine, Lophiobagrus cyclurus, and the brood‐parasite mochokid, Synodontis multipunctatus. Our results indicated contrasting patterns between these species, with strong lake‐wide phylogeographic signal in L. cyclurus including a deep divergence between the northern and southern lake basins. Further structuring of these populations was observed across a heterogeneous habitat over much smaller distances. Strong population growth was observed in L. cyclurus sampled from shallow shorelines, suggesting population growth associated with the colonization of new habitats following lake‐level rises. Conversely, S. multipunctatus, which occupies a broader depth range, showed little phylogeographic structure and lower rates of population growth. Our findings suggest that isolation by distance and/or habitat barriers may play a role in the divergence of non‐cichlid fishes in LT, but this effect varies by species.     

Contrasting patterns of phylogeographic relationships in sympatric sister species of ironclad beetles (Zopheridae: <Emphasis Type="Italic">Phloeodes</Emphasis> spp.) in California's Transverse Ranges

Background  

Comparative phylogeography of sympatric sibling species provides an opportunity to isolate the effects of geography and demographics on the evolutionary history of two lineages over the same, known time scale. In the current study, we investigated the phylogeographic structure of two zopherid beetle species, Phloeodes diabolicus and P. plicatus, where their ranges overlap in California's Transverse Ranges.     

Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

Phylogeographic inference can determine the timing of population divergence, historical demographic processes, patterns of migration, and when extended to multiple species, the history of communities. Single‐locus analyses can mislead interpretations of the evolutionary history of taxa and comparative analyses. It is therefore important to revisit previous single‐locus phylogeographic studies, particularly those that have been used to propose general patterns for regional biotas and the processes responsible for generating inferred patterns. Here, we employ a multilocus statistical approach to re‐examine the phylogeography of Lampropeltis zonata. Using nonparametic and Bayesian species delimitation, we determined that there are two well‐supported species within L. zonata. Ecological niche modelling supports the delimitation of these taxa, suggesting that the two species inhabit distinct climatic environments. Gene flow between the two taxa is low and appears to occur unidirectionally. Further, our data suggest that gene flow was mediated by females, a rare pattern in snakes. In contrast to previous analyses, we determined that the divergence between the two lineages occurred in the late Pliocene (c. 2.07 Ma). Spatially and temporally, the divergence of these lineages is associated with the inundation of central California by the Monterey Bay. The effective population sizes of the two species appear to have been unaffected by Pleistocene glaciation. Our increased sampling of loci for L. zonata, combined with previously published multilocus analyses of other sympatric species, suggests that previous conclusions reached by comparative phylogeographic studies conducted within the California Floristic Province should be reassessed.     

Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species,the African forest elephant (Loxodonta cyclotis)

The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants (Loxodonta cyclotis) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male‐mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male‐mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.     

Phylogeography of the burnet moth Zygaena transalpina complex: molecular and morphometric differentiation suggests glacial refugia in Southern France,Western France and micro‐refugia within the Alps

Patterns of common recolonization routes from glacial refugia to Central Europe during the Pleistocene are generalized to paradigms of postglacial recolonization in Europe. Recent studies indicate, however, that the actual phylogeographic history of many species might be more complex and cannot be simplified to generalized patterns. Burnet moths of the Zygaena transalpina complex represent a group of closely related taxa, which are considered as a typical example for these generalized patterns. At present, three groups are recognized that are assumed to have spread from three classical refugia in Western Europe, Italy and the Balkans to Central Europe. Here, we re‐investigate their phylogeography using a combined molecular and morphometric approach. Phylogenetic and nested clade phylogeographic analyses of 476 samples from 55 localities taken from Southern and Central Europe reveal that the Zygaena transalpina complex consists of three distinct haplotype clusters, which geographically roughly correspond to possible refugia in Western Europe, Italy and the Balkans. A synthesis of the data with a geometric morphometry dataset of 425 specimens from 46 localities corroborates this molecular result but differs in several aspects. Important new aspects are multiple refugia of the western ‘hippocrepidis’ branch and micro‐habitats within the Alps of the central ‘transalpina’ branch. Further, our results display a more complex phylogeographic pattern for this species complex, which is not tractable with a rigid, generalized pattern.     

Comparative rangewide phylogeography of four endemic Taiwanese bat species

Phylogeographic reconstructions of codistributed taxa can help reveal the interplay between abiotic factors, such as altitude and climate, and species‐specific attributes, in shaping patterns of population genetic structure. Recent studies also demonstrate the value of both rangewide sampling and species distribution modelling (SDM) in comparative phylogeography. Here, we combine these approaches to study the population histories of four phylogenetically related forest‐dependent bat species. All are endemic to the mountainous island of Taiwan but show differences in their tolerance to altitude, with Murina gracilis considered to be a high‐altitude specialist, M. recondita and Kerivoula sp. low‐altitude specialists, and M. puta an altitudinal generalist. We tested the prediction that contrasting habitat preferences would impact on patterns of past and contemporary gene flow and found broad concordance between the results of population genetic analyses and species distribution models based on the Model for Interdisciplinary Research on Climate. Both lowland species showed evidence of genetic divergence between the east and west of the island, consistent with SDMs that indicated the Central Mountain Range (CMR) has presented a long‐term and continuous barrier to gene flow since before the Last Glacial Maximum. In contrast, Murina gracilis and M. puta showed lower degrees of historical isolation and genetic differentiation associated with the CMR, reflecting greater gene flow, possibly coupled with past population growth in M. puta. Together our results highlight the usefulness of combining distribution models with phylogeographic analyses to understand the drivers of genetic structure.     

Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)?

Life traits such as reproductive strategy can be determining factors of species evolutionary history and explain the resulting diversity patterns. This can be investigated using phylogeographic analyses of genetic units. In this work, the genetic structure of five asteroid genera with contrasting reproductive strategies (brooding: Diplasterias, Notasterias and Lysasterias versus broadcasting: Psilaster and Bathybiaster) was investigated in the Southern Ocean. Over 1,400 mtDNA cytochrome C oxidase subunit I (COI) sequences were analysed using five species delineation methods (ABGD, ASAP, mPTP, sGMYC and mGMYC), two phylogenetic reconstructions (ML and BA), and molecular clock calibrations, in order to examine the weight of reproductive strategy in the observed differences among phylogeographic patterns. We hypothesised that brooding species would show higher levels of genetic diversity and species richness along with a clearer geographic structuring than broadcasting species. In contrast, genetic diversity and species richness were not found to be significantly different between brooders and broadcasters, but broadcasters are less spatially structured than brooders supporting our initial hypothesis and suggesting more complex evolutionary histories associated to this reproductive strategy. Broadcasters' phylogeography can be explained by different scenarios including deep‐sea colonisation routes, bipolarity or cosmopolitanism, and sub‐Antarctic emergence for the genus Bathybiaster; Antarctic‐ New Zealand faunal exchanges across the Polar Front for the genus Psilaster. Brooders' phylogeography could support the previously formulated hypothesis of a past trans‐Antarctic seaway established between the Ross and the Weddell seas during the Plio‐Pleistocene. Our results also show, for the first time, that the Weddell Sea is populated by a mixed asteroid fauna originating from both the East and West Antarctic.     

How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia and their concordance with other codistributed taxa

Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pliocene–Pleistocene glaciation–deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study, we estimated time‐calibrated phylogenetic/phylogeographic patterns in lizards of the Liolaemus lineomaculatus group and relate them to historical Miocene‐to‐Pleistocene events of Patagonia and the previously proposed phylogeographic patterns. Individuals from 51 localities were sequenced for the mitochondrial marker (cyt‐b) and a subsample of individuals from each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one slow evolving mitochondrial gene (12S). Our analyses revealed strong phylogeographic structure among lineages and, in most cases, no signal of demographic changes through time. The lineomaculatus group is composed of three strongly supported clades (lineomaculatus, hatcheri and kolengh + silvanae), and divergence estimates suggested their origins associated with the oldest known Patagonian glaciation (7–5 Ma); subsequent diversification within the lineomaculatus clade coincided with the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade includes nine strongly genetically and geographically structured lineages, five of which are interpreted as candidate species. Our findings suggest that some Liolaemus lineages have persisted in situ, each of them in a different refugium, through several glaciation–deglaciation cycles without demographic fluctuations. We also summarize and update qualitative evidence of some shared phylogeographic breaks and refugia among plants, rodents and lizards.     

Integrative taxonomy and evolutionary history of a newly revealed spider Dysdera ninnii complex (Araneae: Dysderidae)

The spider genus Dysdera is a species‐rich clade of specialized woodlice predators, composed typically of complexes of sibling species. Here, we analyse the Dysdera ninnii complex, distinguishing three species that exhibit slight but constant differences in the morphology of their copulatory organs, and in their genetic background. We designate a neotype for D. ninnii and redescribe it. We consider Dysdera pavesii Thorell, 1873 to be a junior synonym of Dysdera ninnii Canestrini, 1868. In addition, we describe two new species ( D ysdera moravica sp. nov. and D ysdera microdonta sp. nov. ). All three species occur in the region of north‐eastern Italy, Slovenia, and north‐western Croatia. D ysdera moravica sp. nov. expanded to central Europe. The species occur allopatrically or parapatrically. All three species possess the same diploid number and X0 sex chromosome determination. In some individuals we found chromosome fusions, and such polymorphism is common in spiders with holokinetic chromosomes. The analysis of mitochondrial (cytochrome c oxidase subunit I, COI) and nuclear ribosomal (internal transcribed spacer 2, ITS2) DNA markers revealed two clades, one formed by D. ninnii and D . microdonta sp. nov. , and a second by D . moravica sp. nov. Species of the first clade are not well defined by DNA markers. We noticed only weak separation of maternally inherited COI, and even overlap of autosomally inherited ITS2 sequences. We suggest that either short speciation time, unfinished lineage sorting, or rare hybridization events caused this pattern. In one sample of D . microdonta sp. nov. we detected the coxA gene of a Rickettsia species, which is the first record of this parasitic bacteria from the spider family Dysderidae. D ysdera microdonta sp. nov. occurs at higher altitudes than D. ninnii, and their distribution ranges form a long contact zone. Remarkably, we did not record any overlap of the two distribution ranges, suggesting that the lack of a precopulatory interspecific barrier causes a loss of reproduction potential. We hypothesize that because of the unsolved interspecific barrier together with only tiny differences in morphology and COI sequences, and no differences in karyotypes and ITS2 sequences, the D. ninnii species complex is evolutionarily young. © 2014 The Linnean Society of London     

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito‐nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation–migration analyses, however, revealed near‐zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.     

Phylogeography,colonization and population history of the Midas cichlid species complex (<Emphasis Type="Italic">Amphilophus</Emphasis> spp.) in the Nicaraguan crater lakes

Background  

Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.     

Life‐history predicts past and present population connectivity in two sympatric sea stars

Life‐history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic‐developing sea star, Parvulastra exigua, has lower levels of within‐ and among‐population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima (LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic‐developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic‐developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post‐Pleistocene introgression.     

A complex scenario of glacial survival in Mediterranean and continental refugia of a temperate continental vole species (Microtus arvalis) in Europe

The role of glacial refugia in shaping contemporary species distribution is a long-standing question in phylogeography and evolutionary ecology. Recent studies are questioning previous paradigms on glacial refugia and postglacial recolonization pathways in Europe, and more flexible phylogeographic scenarios have been proposed. We used the widespread common vole Microtus arvalis as a model to investigate the origin, locations of glacial refugia, and dispersal pathways, in the group of “Continental” species in Europe. We used a Bayesian spatiotemporal diffusion analysis (relaxed random walk model) of cytochrome b sequences across the species range, including newly collected individuals from 10 Iberian localities and published sequences from 68 localities across 22 European countries. Our data suggest that the species originated in Central Europe, and we revealed the location of multiple refugia (in both southern peninsulas and continental regions) for this continental model species. Our results confirm the monophyly of Iberian voles and the pre-LGM divergence between Iberian and European voles. We found evidence of restricted postglacial dispersal from refugia in Mediterranean peninsulas. We inferred a complex evolutionary and demographic history of M. arvalis in Europe over the last 50,000 years that does not adequately fit previous glacial refugial scenarios. The phylogeography of M. arvalis provides a paradigm of ice-age survival of a temperate continental species in western and eastern Mediterranean peninsulas (sources of endemism) and multiple continental regions (sources of postglacial spread). Our findings also provide support for a major role of large European river systems in shaping geographic boundaries of M. arvalis in Europe.     

Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

Sympatric tree species are subject to similar climatic drivers, posing a question as to whether they display comparable adaptive responses. However, no study has explicitly examined local adaptation of co‐occurring parasitic and autotrophic plant species to the abiotic environment. Here we test the hypotheses that a generalist parasitic tree would display a weaker signal of selection and that genomic variation would associate with fewer climatic variables (particularly precipitation) but have similar spatial patterns to a sympatric autotrophic tree species. To test these hypotheses, we collected samples from 17 sites across the range of two tree species, the hemiparasite Nuytsia floribunda (n = 264) and sympatric autotroph Melaleuca rhaphiophylla (n = 272). We obtained 5,531 high‐quality genome‐wide single nucleotide polymorphisms (SNPs) for M. rhaphiophylla and 6,727 SNPs for N. floribunda using DArTseq genome scan technology. Population differentiation and environmental association approaches were used to identify signals of selection. Generalized dissimilarly modelling was used to detect climatic and spatial patterns of local adaptation across climatic gradients. Overall, 322 SNPs were identified as putatively adaptive for the autotroph, while only 57 SNPs were identified for the parasitic species. We found genomic variation to associate with different sets of bioclimatic variables for each species, with precipitation relatively less important for the parasite. Spatial patterns of predicted adaptive variability were different and indicate that co‐occurring species with disparate life history traits may not respond equally to selective pressures (i.e., temperature and precipitation). Together, these findings provide insight into local adaptation of sympatric parasitic and autotrophic tree species to abiotic environments.     

Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted,independent, or multiple evolutionary responses?

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted‐response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent‐response hypothesis”); or (3) multiple responses (“multiple‐response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co‐occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer‐scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation‐with‐migration models estimated incongruent timelines of among‐region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid‐Pleistocene while P. gillii populations diverged over mid‐late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B₁₀] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple‐response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer‐scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.     

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.     

Comparative phylogeography of codistributed aquatic insects in western North America: insights into dispersal and regional patterns of genetic structure

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Comparing RADseq and microsatellites to infer complex phylogeographic patterns,an empirical perspective in the Crucian carp,Carassius carassius,L.

The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site‐associated DNA sequencing (RADseq) is increasingly used for such applications; however, RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade‐off has previously been examined using simulation studies; however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These data sets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns, showing the existence of two previously unidentified C. carassius lineages in Europe: one found throughout northern and central‐eastern European drainages and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 m years and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with approximate Bayesian computation to show that the postglacial colonization routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology.     

Comparative phylogeography reveals pre‐decline population structure of New Zealand Cyclodina (Reptilia: Scincidae) species

We examined the comparative phylogeography of all species within the endemic New Zealand skink genus Cyclodina to gain insight into the influence of historical processes on the biogeography of the North Island fauna. Until 1–2 kya, six Cyclodina species occurred sympatrically across the North Island of New Zealand. However, most species have undergone dramatic distributional declines subsequent to the introduction of mammals and the arrival of humans. We compare the phylogeographic patterns evident in Cyclodina species in three biogeographic categories: widespread species (Cyclodina aenea, Cyclodina ornata), North Island disjunct relics (Cyclodina macgregori, Cyclodina whitakeri), and northeastern island relics (Cyclodina alani, Cyclodina oliveri, Cyclodina townsi). Mitochondrial DNA (ND2) sequence data was obtained from across the entire range of each Cyclodina species. We used Neighbour‐joining, maximum likelihood and Bayesian methods to examine the phylogeographic patterns present in each species. Phylogeographic patterns varied among species in different biogeographic categories. Substantial phylogeographic structure was evident in the two widespread species (C. aenea, C. ornata), with Pliocene and Pleistocene divergences between clades evident. Divergences among island groups in the three northeastern island relic species (C. alani, C. oliveri, C. townsi) occurred during the late Pliocene–Pleistocene. By contrast, relatively shallow structure, indicative of late Pleistocene divergences, was present in the two North Island disjunct species (C. macgregori, C. whitakeri). The results strongly suggest that the Poor Knights Islands population of C. ornata represents a new species. We suggest that the contrasting phylogeographic patterns exhibited by Cyclodina species in different biogeographic categories might be related to body size, ecology, and habitat preferences. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 388–408.