A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus)

Interpretations of phylogeographic patterns can change when analyses shift from single gene-tree to multilocus coalescent analyses. Using multilocus coalescent approaches, a species tree and divergence times can be estimated from a set of gene trees while accounting for gene-tree stochasticity. We utilized the conceptual strengths of a multilocus coalescent approach coupled with complete range-wide sampling to examine the speciation history of a broadly distributed, North American warm-desert toad, Anaxyrus punctatus. Phylogenetic analyses provided strong support for three major lineages within A. punctatus. Each lineage broadly corresponded to one of three desert regions. Early speciation in A. punctatus appeared linked to late Miocene-Pliocene development of the Baja California peninsula. This event was likely followed by a Pleistocene divergence associated with the separation of the Chihuahuan and Sonoran Deserts. Our multilocus coalescent-based reconstruction provides an informative contrast to previous single gene-tree estimates of the evolutionary history of A. punctatus.     

Deep genealogies and the mid-peninsular seaway of Baja California

Geological forces and long-term climate changes can have profound effects on species. Such effects may be manifested in the pattern and magnitude of genealogical diversity, as revealed by mitochondrial DNA (mtDNA) lineages. The relative importance of the different forces on a regional biota must be evaluated along with a good understanding of geological and climatological history. The peninsula of Baja California of north-western Mexico is one area where both geology and climate have affected the historical biogeography of the regional biota. Molecular studies based on the genealogical relationships among mtDNA lineages have contributed greatly towards elucidating the historical biogeography of Baja California. Perhaps most noticeably, numerous concordant breaks in mtDNA genealogies half-way along the peninsula suggest a vicariant history in which the mid-peninsula was temporarily submerged. This vicariant explanation has recently been criticized, as no conclusive geological evidence exists for a continuous submergence of the mid-peninsula. As an alternative, a scenario based on climatological factors has been suggested. Here we discuss the validity of the hypothesized mid-peninsular vicariance event and the climate-based alternative in explaining the concordant genealogical breaks. We argue that, despite the significant changes in climate brought about by the glacial cycles throughout the Quaternary, a vicariant history involving a mid-peninsular seaway remains the most parsimonious explanation of the observed patterns in mtDNA genealogies.     

Sky island diversification meets the multispecies coalescent – divergence in the spruce‐fir moss spider (Microhexura montivaga,Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

Microhexura montivaga is a miniature tarantula‐like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce‐fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear‐only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic‐scale data sets are gathered for taxa found in naturally fragmented habitats.     

Evolutionary History of the Morocco lizard-Fingered Geckos of the <Emphasis Type="Italic">Saurodactylus brosseti</Emphasis> Complex

Studies of biodiversity in the Maghreb have revealed high genetic diversity and divergent genetic lineages among many taxa including squamates. Geographic barriers such as the Atlas Mountains are one of the key factors promoting genetic differentiation and the high levels of endemism. The lizard-fingered gecko Saurodactylus brosseti is endemic to Morocco. Its range includes both sides of the Atlas Mountains, and although high diversity was previously identified within the species, much of the range was unsampled. To understand the evolutionary and biogeographical history of this species, we used mitochondrial and nuclear DNA sequence data from 64 populations sampled across the entire species range. We employed phylogenetic methods based on gene trees and species trees as well as a time calibrated Bayesian genealogy and coalescent species delimitation approaches. We uncovered four highly divergent and allopatric mitochondrial lineages that did not share haplotypes at variable nuclear loci, suggesting the four groups have been evolving independently since the Miocene, according to our molecular dating estimates. These results coupled with the geographic pattern of genetic diversity suggest a possible role of the Atlas Mountains for the divergence observed between the four lineages of S. brosseti, while each lineage probably later underwent several episodes of fragmentation followed by (re-) expansion during Pleistocene climatic oscillations. Bayesian species delimitation analysis indicates that the four lineages may well be distinct species but we suggest that detailed morphological analyses are needed prior to taxonomic changes. The four lineages represent ancient independent evolutionary units, and deserve conservation management as distinct entities.     

Testing hypotheses for genealogical discordance in a rainforest lizard

Genealogical discordance, or when different genes tell distinct stories although they evolved under a shared history, often emerges from either coalescent stochasticity or introgression. In this study, we present a strong case of mito‐nuclear genealogical discordance in the Australian rainforest lizard species complex of Saproscincus basiliscus and S. lewisi. One of the lineages that comprises this complex, the Southern S. basiliscus lineage, is deeply divergent at the mitochondrial genome but shows markedly less divergence at the nuclear genome. By placing our results in a comparative context and reconstructing the lineages' demography via multilocus and coalescent‐based approximate Bayesian computation methods, we test hypotheses for how coalescent variance and introgression contribute to this pattern. These analyses suggest that the observed genealogical discordance likely results from introgression. Further, to generate such strong discordance, introgression probably acted in concert with other factors promoting asymmetric gene flow between the mitochondrial and nuclear genomes, such as selection or sex‐biased dispersal. This study offers a framework for testing sources of genealogical discordance and suggests that historical introgression can be an important force shaping the genetic diversity of species and their populations.     

Geography best explains global patterns of genetic diversity and postglacial co‐expansion in marine turtles

For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion, while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to postglacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial data set encompassing 23 previously identified lineages from all seven marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian model averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.     

Mito‐nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

Many species have Holarctic distributions that extend across Europe, Asia and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW–NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared with the association between mtDNA and nuDNA divergence observed among different species, OW–NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito‐nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within‐species discord. Male‐mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause increased mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation and that more holistic approaches are needed for species delimitation.     

DNA barcoding will often fail to discover new animal species over broad parameter space

With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).     

Comparative phylogeography reveals a shared impact of pleistocene environmental change in shaping genetic diversity within nine Anopheles mosquito species across the Indo-Burma biodiversity hotspot

South-East Asia is one of the world's richest regions in terms of biodiversity. An understanding of the distribution of diversity and the factors shaping it is lacking, yet essential for identifying conservation priorities for the region's highly threatened biodiversity. Here, we take a large-scale comparative approach, combining data from nine forest-associated Anopheles mosquito species and using statistical phylogeographical methods to disentangle the effects of environmental history, species-specific ecology and random coalescent effects. Spatially explicit modelling of Pleistocene demographic history supports a common influence of environmental events in shaping the genetic diversity of all species examined, despite differences in species' mtDNA gene trees. Populations were periodically restricted to allopatric northeastern and northwestern refugia, most likely due to Pleistocene forest fragmentation. Subsequent southwards post-glacial recolonization is supported by a north-south gradient of decreasing genetic diversity. Repeated allopatric fragmentation and recolonization have led to the formation of deeply divergent geographical lineages within four species and a suture zone where these intraspecific lineages meet along the Thai-Myanmar border. A common environmental influence for this divergence was further indicated by strong support for simultaneous divergence within the same four species, dating to approximately 900 thousand years ago (kya). Differences in the geographical structuring of genetic diversity between species are probably the result of varying species' biology. The findings have important implications for conservation planning; if the refugial regions and suture zone identified here are shared by other forest taxa, the unique and high levels of genetic diversity they house will make these areas conservation priorities.     

Recent divergence,intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi‐Atlantic peatmoss populations

Several lines of evidence suggest that recent long‐distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi‐Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (im and migrate ) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F_ST = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long‐range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000–289 000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi‐Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.     

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.     

Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group

Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensisby collecting genetic data (669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence (estimated using MDIV) is 3.75 x 106 years, and the 95%credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. WithinP. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate (g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima's Dand mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the significance of the population growth-rate parameter.     

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

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

Coalescence in a metapopulation with recurrent local extinction and recolonization

Abstract Many species exist as metapopulations in balance between local population extinction and recolonization. The effect of these processes on average population differentiation, within-deme diversity, and specieswide diversity has been considered previously. In this paper, coalescent simulations of Slatkin's propagule-pool and migrant-pool models are used to characterize the distribution of neutral genetic diversity within demes (π_s), diversity in the metapopulation a whole (TT_T), the ratio F _ST= (π_t–π_S)/π_T, Tajima's D statistic, and several ratios of gene-tree branch lengths. Using these distributions, power to detect differences in key metapopulation parameter values is determined under contrasting sampling regimes. The results indicate that it will be difficult to use sequence data from a single locus to detect a history of extinctions and recolonizations in a metapopulation because of high genealogical variance, the loss of diversity due to reductions in effective population size, and the fact that a genealogy of lineages from different demes under Slatkin's model differs from a neutral coalescent only in its time scale. Genetic indices of gene-tree shape that capture the effects of extinction/recolonization on both external branches and the length of the genealogy as a whole will provide the best indication of metapopulation dynamics if several lineages are sampled from several different demes.     

Colour variation is incongruent with mitochondrial lineages: cryptic speciation and subsequent diversification in a Gulf of California reef fish (Teleostei: Blennioidei)

The Gulf of California endemic reef fish, Acanthemblemaria crockeri (Blennioidei, Chaenopsidae), reportedly has two colour morphs, one with melanic lateral spots ('Gulf' morph) and one with orange spots ('Cape' morph). In this study, we recorded colour morph in both males and females and collected mitochondrial DNA sequence data for cytochrome c oxidase I (COI) and tRNA-Pro/D-loop of specimens from throughout the Gulf to explore the genetic basis of the colour morphs. Two highly divergent (HKY + I distance = 11.9% for COI), reciprocally monophyletic lineages were identified, consistent with the presence of two parapatric species. A 30-km gap between the distributions of mitochondrial lineages roughly corresponds to a hypothesized former seaway across the Baja California peninsula north of La Paz, although the estimated divergence time (1.84 million years ago) is more recent than the hypothetical seaway (3–4 million years ago). Surprisingly, the distribution of mitochondrial species is not congruent with the distribution of either male or female colour morphs. Our analysis also revealed significant population differentiation within both species and no shared haplotypes among populations. The northern Gulf species includes four populations (NB, CB, NM and CM) corresponding to northern and central Baja and northern and central mainland sites, while the Cape species includes two populations (SB and SM) corresponding to the Baja and mainland sides of the southern Gulf. The NB/CB division corresponds to a hypothesized Plio–Pleistocene mid-peninsular seaway. The level of genetic divergence documented in this lineage is extraordinary for a marine fish with a pelagic larval stage within a semi-enclosed basin.     

Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species

Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent‐based inferences about demographic processes to reconstruct the population histories of two co‐distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation.     

Diversification of montane species via elevation shifts: the case of the Kaçkar cricket Phonochorion (Orthoptera)

Localized up‐down altitudinal shifts and subsequent isolation–admixture of montane species in response to glacial cycles has been proposed as a mechanism for the high diversity along Anatolian mountains. However, specific predictions of the proposed mechanism (the elevation shift model) have yet to be tested. Here, we provide a first assessment of this model for promoting inter‐ and intraspecific genetic diversity in the bush‐cricket genus Phonochorion endemic to the West Lesser Caucasus hotspot. Mitochondrial genes were analysed by Bayesian Markov Chain Monte Carlo inferences and coalescent simulations. Timing of diversification was estimated using a multispecies coalescent model. Divergence with gene flow was tested using an isolation with migration model. Population genetic parameters and genetic structuring were determined using Bayesian coalescent methods and spatial analysis. Demographic history was assessed using mismatch distributions and extended Bayesian skyline plots. Speciation events corresponded both to the Miocene and Pleistocene while intraspecific divergence was Pleistocene based. There was evidence for moderate levels of gene flow between species during diversification; however, incomplete lineage sorting could explain the data as well as gene flow. Overall diversification patterns within the genus Phonochorion agree with the predictions of the elevations shift model. Genetic patterns of diversification were driven mainly by Pleistocene glacial cycles and reflected the nature and distribution of sky islands. There was also some albeit weak evidence of demographic expansions coinciding with glacial cooling. However, evidence for divergence with gene flow was inconclusive.     

Complexity of the simplest species tree problem

The multispecies coalescent model provides a natural framework for species tree estimation accounting for gene-tree conflicts. Although a number of species tree methods under the multispecies coalescent have been suggested and evaluated using simulation, their statistical properties remain poorly understood. Here, we use mathematical analysis aided by computer simulation to examine the identifiability, consistency, and efficiency of different species tree methods in the case of three species and three sequences under the molecular clock. We consider four major species-tree methods including concatenation, two-step, independent-sites maximum likelihood, and maximum likelihood. We develop approximations that predict that the probit transform of the species tree estimation error decreases linearly with the square root of the number of loci. Even in this simplest case, major differences exist among the methods. Full-likelihood methods are considerably more efficient than summary methods such as concatenation and two-step. They also provide estimates of important parameters such as species divergence times and ancestral population sizes,whereas these parameters are not identifiable by summary methods. Our results highlight the need to improve the statistical efficiency of summary methods and the computational efficiency of full likelihood methods of species tree estimation.     

Shifting distributions and speciation: species divergence during rapid climate change

Questions about how shifting distributions contribute to species diversification remain virtually without answer, even though rapid climate change during the Pleistocene clearly impacted genetic variation within many species. One factor that has prevented this question from being adequately addressed is the lack of precision associated with estimates of species divergence made from a single genetic locus and without incorporating processes that are biologically important as populations diverge. Analysis of DNA sequences from multiple variable loci in a coalescent framework that (i) corrects for gene divergence pre-dating speciation, and (ii) derives divergence-time estimates without making a priori assumptions about the processes underlying patterns of incomplete lineage sorting between species (i.e. allows for the possibility of gene flow during speciation), is critical to overcoming the inherent logistical and analytical difficulties of inferring the timing and mode of speciation during the dynamic Pleistocene. Estimates of species divergence that ignore these processes, use single locus data, or do both can dramatically overestimate species divergence. For example, using a coalescent approach with data from six loci, the divergence between two species of montane Melanoplus grasshoppers is estimated at between 200,000 and 300,000 years before present, far more recently than divergence estimates made using single-locus data or without the incorporation of population-level processes. Melanoplus grasshoppers radiated in the sky islands of the Rocky Mountains, and the analysis of divergence between these species suggests that the isolation of populations in multiple glacial refugia was an important factor in promoting speciation. Furthermore, the low estimates of gene flow between the species indicate that reproductive isolation must have evolved rapidly for the incipient species boundaries to be maintained through the subsequent glacial periods and shifts in species distributions.     

Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy

With the proliferation of species-tree methods, empiricists now have to confront the daunting task of method choice. Such decisions might be made based on theoretical considerations alone. However, the messiness of real data means that theoretical ideals may not hold in practice (e.g., with convergence of complicated MCMC algorithms and computational times that limit analyses to small data sets). On the other hand, simplifying assumptions made by some approaches may compromise the accuracy of species-tree estimates. Here we examine the purported tradeoff between accuracy and computational simplicity for species-tree analysis, focusing on the different ways the approaches treat gene-tree uncertainty. By considering a diversity of species trees, as well as different sampling designs and total sampling efforts, we not only compare the accuracy of species-tree estimates across methods, but we also partition the variation in accuracy across factors to identify their relative importance. This analysis shows that although the method of analysis affects accuracy, other factors - namely, the history of species divergence and aspects of the sampling design - have a larger impact. Despite a full modeling of gene tree uncertainty (e.g., using a Bayesian framework), species-tree estimates may not be accurate, particularly for recent diversification histories. Nevertheless, we demonstrate how factors within the control of the empirical investigator (e.g., decisions about sampling) improve the accuracy of species tree estimates, and more so than the method of analysis. Lastly, with much of the attention on species-tree analyses focused on the discord among loci arising from the coalescent, this work also highlights a previously overlooked key determinant of species-tree accuracy for recent divergences - the level of genetic variation at a locus, which has important implications for improving species-tree estimates in practice.