Hierarchical Approximate Bayesian Computation Research Articles

Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species.

Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.

Individual Differences in Cue Weighting in Sentence Comprehension: An Evaluation Using Approximate Bayesian Computation.

Cue-based retrieval theories of sentence processing assume that syntactic dependencies are resolved through a content-addressable search process. An important recent claim is that in certain dependency types, the retrieval cues are weighted such that one cue dominates. This cue-weighting proposal aims to explain the observed average behavior, but here we show that there is systematic individual-level variation in cue weighting. Using the Lewis and Vasishth cue-based retrieval model, we estimated individual-level parameters for reading speed and cue weighting using 13 published datasets; hierarchical approximate Bayesian computation (ABC) was used to estimate the parameters. The modeling reveals a nuanced picture of cue weighting: we find support for the idea that some participants weight cues differentially, but not all participants do. Only fast readers tend to have the predicted higher weighting for structural cues, suggesting that reading proficiency (approximated here by reading speed) might be associated with cue weighting. A broader achievement of the work is to demonstrate how individual differences can be investigated in computational models of sentence processing without compromising the complexity of the model.

Drivers of unique and asynchronous population dynamics in Malagasy herpetofauna

AbstractAimA long history of isolation coupled with complex landscapes makes Madagascar ideal for exploring the historical factors that have shaped patterns of population diversity and endemism. Many species‐level studies have suggested Late Quaternary climate change may have influenced population dynamics in the tropics, but unique biomes and individual species properties may have driven idiosyncratic responses to these shifts. Here, we use community‐scale population genetic data to investigate the impact of Quaternary climate cycles on shared demographic response and investigate the contributions of both biotic and abiotic factors which shape these demographic trajectories.LocationMadagascar.TaxonReptiles and Amphibians.MethodsUsing community‐scale population genetic data, we implement a hierarchical approximate Bayesian computation approach to evaluate the degree of synchronous population expansion during glacial cycles across herpetofaunal assemblages both within and across discrete biomes and taxonomic groups. We use Bayesian model averaging to identify intrinsic and extrinsic conditions predictive of individualistic demographic change.ResultsWe find that demographic responses are not uniform across groups, with more than 50% of all populations showing signal of recent expansion. Our explanatory models indicate species occupying narrow elevational ranges had a higher probability of expansion, while amphibian assemblages showed higher genetic diversity and greater departures from population neutrality. Expansion events were largely asynchronous, with coexpansion found in less than half of all populations. Exceptionally, 69%–74% of all humid‐restricted populations coexpanded during the start of the Last Glacial Period at around 100 kya, supporting the hypothesis of a more extensive humid forest cover for Madagascar during this time.Main conclusionsWe show that differences in life history and regional biogeography have contributed to patterns of richness and endemism found across Madagascar, and historical connectivity across humid forests has been an important factor in shaping present‐day diversity and endemism on Madagascar, particularly for amphibians.

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography.

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.

Back to the brink: Phylogeography and demographic history of the endangered Torreya jackii

AbstractBoth paleoclimatic change and anthropogenic habitat destruction can have adverse effects on species demography and, in turn, could lead a species towards being endangered and rare. Understanding the relative importance of these natural and anthropogenic factors driving species endangerment and rarity is thus crucial for effective conservation planning but remains elusive. Here, we examine the phylogeography and demographic history of an endangered conifer species in China, Torreya jackii Chun, and assess the relative importance of natural and anthropogenic factors that might have put the species in its endangered state. We collected tissue samples from all the 13 extant wild populations, and analyzed the genetic variation using eight nuclear microsatellites and four chloroplast and one mitochondrial DNA fragments. We found low genetic and nucleotide diversities, which could explain the absence of spatial and phylogeographic structure. Using a hierarchical approximate Bayesian computation technique, we identified the demographic scenario that best fits the genetic data and found that effective population size was low at least 200 000 years ago but expanded after the last glacial maximum (LGM). The paleoclimatic niche model revealed a profound effect of precipitation on the distribution of T. jackii and predicted that the current distribution areas were suitable during the LGM. Despite the post‐LGM expansion, the best‐supported scenario showed a dramatic population collapse during the past 300 years, when anthropogenic disturbances also increased dramatically. Overall, our study sheds light on how historical factors and human impacts jointly threaten the persistence of a species, and these aspects should be duly considered in species conservation planning.

Comparative phylogeographic analysis suggests a shared history among eastern North American boreal forest birds

AbstractPhylogeographic structure within high-latitude North American birds is likely shaped by a history of isolation in refugia during Pleistocene glaciations. Previous studies of individual species have come to diverse conclusions regarding the number and location of likely refugia, but no studies have explicitly tested for biogeographic concordance in a comparative phylogeographic framework. Here we use a hierarchical approximate Bayesian computation analysis of mitochondrial DNA sequences from 653 individuals of 6 bird species that are currently co-distributed in the boreal forest of North America to test for biogeographic congruence. We find support for congruent phylogeographic patterns across species, with shallow divergence dating to the Holocene within each species. Combining genetic results with paleodistribution modeling, we propose that these species shared a single Pleistocene refugium south of the ice sheets in eastern North America. Additionally, we assess modern geographic genetic structure within species, focusing on Newfoundland and disjunct high-elevation populations at the southern periphery of ranges. We find evidence for a “periphery effect” in some species with significant genetic structure among peripheral populations and between peripheral and central populations. Our results suggest that reduced gene flow among peripheral populations, rather than discordant biogeographic histories, can explain the small differences in genetic structure and levels of genetic diversity among co-distributed boreal forest birds.

A Comparative Phylogeographic Approach to Facilitate Recovery of an Imperiled Freshwater Mussel (Bivalvia: Unionida: Potamilus inflatus)

North American freshwaters are among the world’s most threatened ecosystems, and freshwater mussels are among the most imperiled inhabiting these systems. A critical aspect of conservation biology is delineating patterns of genetic diversity, which can be difficult when a taxon has been extirpated from a significant portion of its historical range. In such cases, evaluating conservation and recovery options may benefit by using surrogate species as proxies when assessing overall patterns of genetic diversity. Here, we integrate the premise of surrogate species into a comparative phylogeographic framework to hypothesize genetic relationships between extant and extirpated populations of Potamilus inflatus by characterizing genetic structure in co-distributed congeners with similar life histories and dispersal capabilities. Our mitochondrial and nuclear sequence data exhibited variable patterns of genetic divergence between Potamilus spp. native to the Mobile and Pascagoula + Pearl + Pontchartrain (PPP) provinces. However, hierarchical Approximate Bayesian Computation indicated that the diversification between Mobile and PPP clades was synchronous and represents a genetic signature of a common history of vicariance. Recent fluctuations in sea-level appear to have caused Potamilus spp. in the PPP to form a single genetic cluster, providing justification for using individuals from the Amite River as a source of brood stock to re-establish extirpated populations of P. inflatus. Future studies utilizing eDNA and genome-wide molecular data are essential to better understand the distribution of P. inflatus and establish robust recovery plans. Given the imperilment status of freshwater mussels globally, our study represents a useful methodology for predicting relationships among extant and extirpated populations of imperiled species.

Testing Hypotheses of Diversification in Panamanian Frogs and Freshwater Fishes Using Hierarchical Approximate Bayesian Computation with Model Averaging

Most Neotropical frog and freshwater fish species sampled to date show phylogeographic breaks along the Pacific coast of the Isthmus of Panama, with lineages in Costa Rica and western Panama isolated from central Panama. We examine temporal patterns of diversification of taxa across this ‘western Panama isthmus’ (WPI) break to test hypotheses about the origin of species geographical distributions and genetic structuring in this region. We tested for synchronous diversification of four codistributed frog taxon-pairs and three fish taxon-pairs sharing the WPI break using hierarchical approximate Bayesian computation with model averaging based on mitochondrial DNA sequences. We also estimated lineage divergence times using full-Bayesian models. Several of our results supported synchronous divergences within the frog and freshwater fish assemblages; however, Bayes factor support was equivocal for or against synchronous or asynchronous diversification. Nevertheless, we infer that frog populations were likely isolated by one or multiple Pliocene–Pleistocene events more recently than predicted by previous models, while fish genetic diversity was structured by Pleistocene events. By integrating our results with external information from geology and elevational sea level modeling, we discuss the implications of our findings for understanding the biogeographical scenario of the diversification of Panamanian frogs and fishes. Consistent with the ‘Bermingham/Martin model’ (Molecular Ecology 1998, 7, 499–517), we conclude that the regional fish assemblage was fractured by processes shaping isthmian landscapes during the Pleistocene glaciations, including drainage basin isolation during lowered sea levels.

Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil.

Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.

Strategies for improving approximate Bayesian computation tests for synchronous diversification

BackgroundEstimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization.MethodsThrough simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on Ψ on the estimation of co-divergence variability. We also introduce a new setting (β) that can potentially improve estimation of Ψ by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs.ResultsWe demonstrate that the choice of prior on Ψ has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of β improves estimation of Ψ, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies.ConclusionsOur simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on Ψ has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon-pairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between Ψ and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of co-divergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs.

Asynchronous diversification of snakes in the North American warm deserts

AbstractAimWe quantify the degree to which co‐distributed snakes across the Cochise Filter Barrier (CFB) have a shared history of population divergence and estimate the timing of divergence for each taxon pair.LocationNorth America.MethodsA single locus dataset was collected (n = 747 individuals) for 12 snake taxon pairs. Phylogeographical structure was estimated for each taxon. Redundancy analyses were used to assess the importance of geographical distance, climate and putative barriers to gene flow in structuring genetic diversity. Hierarchical approximate Bayesian computation was used to estimate the magnitude of synchronicity in divergence times across a well‐documented phylogeographical barrier. Lastly, gene divergence and population divergence times were estimated using multiple methods.ResultsThere is substantial phylogeographical structure in many of the snake taxa, particularly at the CFB. A model containing distance, climate and barriers explained the greatest amount of genetic variation in nearly all taxa. When each variable was examined separately, climate explained the most variation. The hABC model testing indicates that there is overwhelming support for asynchronous phylogeographical histories within these co‐distributed taxa. Estimated divergence times range throughout the Quaternary and Neogene.Main ConclusionsWe demonstrate that the 12 snake taxon pairs studied here have diversified within the desert Southwest forming distinct Sonoran and Chihuahuan populations, illustrating the importance of this region in driving diversification in North American taxa. Although these groups exhibit the same pattern of lineage formation, there is strong support for asynchronous diversification and little concordance in divergence time estimates.

A mid-Pleistocene rainforest corridor enabled synchronous invasions of the Atlantic Forest by Amazonian anole lizards.

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large-scale biogeographic patterns and ecological processes. An example is that of transient corridors of suitable habitat across disjunct but ecologically similar regions, which have been associated with climate change over time. Such connections likely played a role in the assembly of tropical communities, especially within the highly diverse Amazonian and Atlantic rainforests of South America. Although these forests are presently separated by open and dry ecosystems, paleoclimatic and phylogenetic evidence suggest that they have been transiently connected in the past. However, little is known about the timing, magnitude and the distribution of former forest connections. We employ sequence data at multiple loci from three codistributed arboreal lizards (Anolis punctatus, Anolis ortonii and Polychrus marmoratus) to infer the phylogenetic relationships among Amazonian and Atlantic Forest populations and to test alternative historical demographic scenarios of colonization and vicariance using coalescent simulations and approximate Bayesian computation (ABC). Data from the better-sampled Anolis species support colonization of the Atlantic Forest from eastern Amazonia. Hierarchical ABC indicates that the three species colonized the Atlantic Forest synchronously during the mid-Pleistocene. We find support of population bottlenecks associated with founder events in the two Anolis, but not in P.marmoratus, consistently with their distinct ecological tolerances. Our findings support that climatic fluctuations provided key opportunities for dispersal and forest colonization in eastern South America through the cessation of environmental barriers. Evidence of species-specific histories strengthens assertions that biological attributes play a role in responses to shared environmental change.

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.

Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island Complex.

The contribution of Pleistocene sea level changes to diversification patterns in archipelagos around the world, and specifically whether the repeated cycles of island connectivity and isolation acted as a 'species pump' is debated. The debate has been perpetuated in part because of the type of evidence used to evaluate the species-pump hypothesis. Specifically, existing tests of the 'Pleistocene Aggregate Island Complex' (PAIC) model of diversification interpret the lack of concordant divergence times among multiple codistributed taxa as a rejection of the PAIC model. However, the null expectation of concordance disregards taxon-specific ecological traits and geographic characteristics that may affect population persistence and gene flow among islands. Here, we study the factors affecting population divergence in thirteen flightless darkling beetle species (Coleoptera: Tenebrionidae) across the PAIC system of the Cycladic plateau in the Aegean archipelago. Based on isolation-by-resistance analyses, hierarchical amova and the degree of genealogical sorting on individual islands, we identify a major effect of bathymetry and habitat stability on the levels of genetic divergence across the PAIC, with island size and body size playing a secondary role as well. We subsequently use bathymetric maps and habitat association to generate predictions about the set of islands and group of taxa expected to show phylogeographic concordance. We test these predictions using hierarchical approximate Bayesian computation and show how our interpretations regarding the role of PAICs as drivers of divergence change when relying on a null expectation of concordance compared to a refined model that takes geography and ecological traits into account.

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.

Comparative phylogeography highlights the double-edged sword of climate change faced by arctic- and alpine-adapted mammals.

Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.

Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate.

Comparative Phylogeographic Analyses Illustrate the Complex Evolutionary History of Threatened Cloud Forests of Northern Mesoamerica

Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests–among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.

A species assemblage approach to comparative phylogeography of birds in southern Australia

We present a novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data. We use coalescent-based hierarchical approximate Bayesian computation (HABC) methods (MsBayes) to estimate the number and timing of discrete divergences across a putative barrier and to assign species to their appropriate period of co-divergence. We then apply a coalescent-based full Bayesian model of divergence (IMa) to suites of species shown to have simultaneously diverged. The full Bayesian model results in reduced credibility intervals around divergence times and allows other parameters associated with divergence to be summarized across species assemblages. We apply this approach to 10 bird species that are wholly or patchily discontinuous in semi-arid habitats between Australia's southwest (SW) and southeast (SE) mesic zones. There was substantial support for up to three discrete periods of divergence. HABC indicates that two species wholly restricted to more mesic habitats diverged earliest, between 594,382 and 3,417,699 years ago, three species from semi-arid habitats diverged between 0 and 1,508,049 years ago, and four diverged more recently, between 0 and 396,843 years ago. Eight species were assigned to three periods of co-divergence with confidence. For full Bayesian analyses, we accounted for uncertainty in the two remaining species by analyzing all possible suites of species. Estimates of divergence times from full Bayesian divergence models ranged between 429,105 and 2,006,355; 67,172 and 663,837; and 24,607 and 171,085 for the earliest, middle, and most recent periods of co-divergence, respectively. This single-locus approach uses the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research using multilocus and genomic tools applied to an understudied biome.

Historical biogeography of the Brazilian Atlantic forest and the Carnaval-Moritz model of Pleistocene refugia: what do phylogeographical studies tell us?

The present study uses published phylogeographical studies to test the Carnaval–Moritz (CM) model of forest dynamics in the Atlantic forest of Brazil. The model predicts that a large forested area in the north–central region of this biome has remained stable during the last glacial maximum, and only relicts in its current southernmost distributions. All available sequences for phylogeographical studies on vertebrates on the Atlantic forest were obtained from GenBank. All datasets consisted of mitochondrial sequences and were submitted to the same analyses, including time of divergence and migration rates between phylogeographical lineages, as well as historical demography analyses, including neutrality tests and Ne estimates. The species studied showed different degrees of phylogeographical structure. Two contact zones are defined: one very heterogeneous in south-east Brazil that was largely congruent with the CM model and one around the Doce river further north. Population genetics analyses showed a smaller effective number on southern population, and most of these southern populations showed evidence for recent demographic expansion. These features are also in agreement with the CM model. Additionally, divergence/expansion events dated back to the Pleistocene epoch in all but one organism. According to hierarchical approximate Bayesian computation analysis, most of the data can be attributed to a single event. The results highlight the need for more finescale studies in the Atlantic forest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 499–509.