Inferring responses to climate dynamics from historical demography in neotropical forest lizards

Dragons in the tropics - Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa

Co-distributed taxa can respond both similarly or differently to the same climatic and geological events, resulting in a range of phylogeographic patterns across the region. Using a nested approach on a taxonomically diverse yet morphologically conservative group of agamid lizards, we first aimed to evaluate more precisely the extent of phylogeographic structuring within the genus. Then, focusing on four lineages within the more widespread species, we assessed the impact of biogeographic barriers on phylogeographic structuring and demographic history of species, comparing to patterns previously observed in co-distributed taxa. These species occur in the Australian Monsoonal Tropics, a vast tropical savanna system with high richness and endemism associated with environmental heterogeneity and past climate fluctuations. The employment of genomic data helped to determine the relationships between specific taxa that were previously difficult to place. We found a local influence of biogeographic and climatic breaks on population dynamics, analogous to other species. We detected high levels of population structure in the West Kimberley and Arnhem Plateau, which are already known for high endemism. However, we also highlighted unique lineages in areas that have been overlooked until recently, in the South Kimberley and West Top End. Climatic and geographical features in the Arnhem Plateau act as a soft barrier between populations in the east and west regions of the Top End. These observations reflect patterns observed for other vertebrates across this rich biome, indicating how climatic variation, species' ecology, and landscape features interact to shape regional diversity and endemism.

Drivers of genomic differentiation landscapes in populations of disparate ecological and geographical settings within mainland Apis cerana

Elucidating the evolutionary processes that drive population divergence can enhance our understanding of the early stages of speciation and inform conservation management decisions. The honeybee Apis cerana displays extensive population divergence, providing an informative natural system for exploring these processes. The mainland lineage A. cerana includes several peripheral subspecies with disparate ecological and geographical settings radiated from a central ancestor. Under this evolutionary framework, we can explore the patterns of genome differentiation and the evolutionary models that explain them. We can also elucidate the contribution of non-genomic spatiotemporal mechanisms (extrinsic features) and genomic mechanisms (intrinsic features) that influence these genomic differentiation landscapes. Based on 293 whole genomes, a small part of the genome is highly differentiated between central-peripheral subspecies pairs, while low and partial parallelism partly reflects idiosyncratic responses to environmental differences. Combined elements of recurrent selection and speciation-with-gene-flow models generate the heterogeneous genome landscapes. These elements weight differently between central-island and other central-peripheral subspecies pairs, influenced by glacial cycles superimposed on different geomorphologies. Although local recombination rates exert a significant influence on patterns of genomic differentiation, it is unlikely that low-recombination rates regions were generated by structural variation. In conclusion, complex factors including geographical isolation, divergent ecological selection and non-uniform genome features have acted concertedly in the evolution of reproductive barriers that could reduce gene flow in part of the genome and facilitate the persistence of distinct populations within mainland lineage of A. cerana.

Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia

Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.

Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests

An open and dry vegetation belt separates Amazonia (AM) and the Atlantic Forest (AF). Evidence from palaeoclimatic and phylogenetic studies suggests past connections between these forests during cycles of increased humidity through the formation of forest corridors. The distinctive northern AF avifauna is known to have affinities both with AM and the southern AF. Still, the extent of how these two regions contributed to the assemblage of this avifauna remains poorly understood. Using historical demographic analyses and comparative phylogeography based on sub-genomic genetic sampling, we assessed how past connections between AM and AF led to shared vicariance and colonization events in four avian AF endemic taxa. Our results supported the occurrence of humid forest corridors promoting the contact between AF and AM populations and suggested two vicariant events and two colonization events from AF to AM. Population divergences were mostly non-synchronous and occurred multiple times during the Pleistocene. Historical gene flow was prevalent across study groups, supporting migration flows after the initial separation between AM and AF - a pattern previously unknown in birds between these regions. Idiosyncratic histories and divergent demographic syndromes suggest that organisms' responses to climate-driven habitat shifts broadly depend on their ecological attributes. This study strengthened our knowledge of past connections between AM and AF and provided demographic scenarios amenable for testing in other groups of co-distributed organisms.

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.

Successive climate crises in the deep past drove the early evolution and radiation of reptiles

Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.

Phylogeography of a Typical Forest Heliothermic Lizard Reveals the Combined Influence of Rivers and Climate Dynamics on Diversification in Eastern Amazonia

The formation of the Amazon drainage basin has been considered an important driver of speciation of several taxa, promoting vicariant events or reinforcement of barriers that restrict gene flow between opposite river margins. Several recent studies reported a set of miscellaneous events involving climatic fluctuations, geomorphological changes, and dispersal mechanisms as propellers of diversification of Amazonian rainforest taxa. Here, we show the results of dated phylogenetic, biogeographic, and populational analyses to investigate which events could better explain the current distribution of a heliothermic, active foraging lizard in the central and eastern portions of the Amazonian rainforest (besides a disjunct distribution in part of the Atlantic Forest). We sampled Kentropyx calcarata from most of its area of occurrence in Amazonia and used mitochondrial and nuclear markers to evaluate if the genetic structure agrees with evolutionary scenarios previously proposed for Amazonia. We performed phylogenetic and populational analyses to better understand the dynamics of this species in the Amazonia rainforest over time. Phylogenetic inference recovered ten K. calcarata structured lineages in eastern Amazonia, some of them limited by the Amazon River and its southern tributaries (Tapajós, Xingu, and Tocantins), although we detected occasional haplotype sharing across some of the river banks. According to molecular dating, K. calcarata diversified since Miocene–Pliocene, and some of the lineages presented signs of demographic expansion during the Pleistocene, supposedly triggered by climatic dynamics. The putative ancestral lineage of K. calcarata was distributed on the Guiana Shield, later spreading south and southeastward by dispersion. Our results indicate that Amazonian rivers acted as barriers to the dispersal of Kentropyx calcarata, but they were not the sole drivers of diversification.

Phylogenomic analysis of evolutionary relationships in Ranitomeya poison frogs (Family Dendrobatidae) using ultraconserved elements

The use of genome-scale data in phylogenetics has enabled recent strides in determining the relationships between taxa that are taxonomically problematic because of extensive morphological variation. Here, we employ a phylogenomic approach to infer evolutionary relationships within Ranitomeya (Anura: Dendrobatidae), an Amazonian lineage of poison frogs consisting of 16 species with remarkable diversity in color pattern, range size, and parental care behavior. We infer phylogenies with all described species of Ranitomeya from ultraconserved nuclear genomic elements (UCEs) and also estimate divergence times. Our results differ from previous analyses regarding interspecific relationships. Notably, we find that R. toraro and R. defleri are not sister species but rather distantly related, contrary to previous analyses based on smaller genetic datasets. We recover R. uakarii as paraphyletic, designate certain populations formerly assigned to R. fantastica from Peru as R. summersi, and transfer the French Guianan and eastern Brazilian R. amazonica populations to R. variabilis. By clarifying both inter- and intraspecific relationships within Ranitomeya, our study paves the way for future tests of hypotheses on color pattern evolution and historical biogeography.

A multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic Forest hotspot

Abstract: We briefly describe selected results from our thematic project focused on the biodiversity of the Atlantic Forest (“AF BIOTA”), which was jointly funded by FAPESP’s BIOTA Program, the U.S. National Science Foundation Dimensions of Biodiversity Program, and the National Aeronautics and Space Administration (NASA). As one of the five most important hotspots of biodiversity in the world, the Atlantic Forest (AF) holds less than 16% of its vegetation cover, yet, amongst the hotspots, it still harbors one of the highest numbers of species, including endemics. By gathering specialists across multiple disciplines (biology, geology, engineering), we aimed to understand how this megabiodiversity was built through time, informing biodiversity science and conservation. Among the results, we trained 18 Master’s and 26 Ph.D. students, published more than 400 peer-reviewed papers that improved our knowledge about the forest’s biologic and climatic diversity and dynamics through time, developed new analytical methods, produced outreach videos and articles, and provided data to help define biodiversity conservation policies.

Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)

The effects of genetic introgression on species boundaries and how they affect species' integrity and persistence over evolutionary time have received increased attention. The increasing availability of genomic data has revealed contrasting patterns of gene flow across genomic regions, which impose challenges to inferences of evolutionary relationships and of patterns of genetic admixture across lineages. By characterizing patterns of variation across thousands of genomic loci in a widespread complex of true toads (Rhinella), we assess the true extent of genetic introgression across species thought to hybridize to extreme degrees based on natural history observations and multi-locus analyses. Comprehensive geographic sampling of five large-ranged Neotropical taxa revealed multiple distinct evolutionary lineages that span large geographic areas and, at times, distinct biomes. The inferred major clades and genetic clusters largely correspond to currently recognized taxa; however, we also found evidence of cryptic diversity within taxa. While previous phylogenetic studies revealed extensive mito-nuclear discordance, our genetic clustering analyses uncovered several admixed individuals within major genetic groups. Accordingly, historical demographic analyses supported that the evolutionary history of these toads involved cross-taxon gene flow both at ancient and recent times. Lastly, ABBA-BABA tests revealed widespread allele sharing across species boundaries, a pattern that can be confidently attributed to genetic introgression as opposed to incomplete lineage sorting. These results confirm previous assertions that the evolutionary history of Rhinella was characterized by various levels of hybridization even across environmentally heterogeneous regions, posing exciting questions about what factors prevent complete fusion of diverging yet highly interdependent evolutionary lineages.

Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude

The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical-geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a tradeoff between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, that is, significant phylogenetic niche conservatism. We rejected the tradeoff hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.

Distinct interspecific and intraspecific vulnerability of coastal species to global change

Characterising and predicting species responses to anthropogenic global change is one of the key challenges in contemporary ecology and conservation. The sensitivity of marine species to climate change is increasingly being described with forecasted species distributions, yet these rarely account for population level processes such as genomic variation and local adaptation. This study compares inter- and intraspecific patterns of biological composition to determine how vulnerability to climate change, and its environmental drivers, vary across species and populations. We compare species trajectories for three ecologically important southern African marine invertebrates at two time points in the future, both at the species level, with correlative species distribution models, and at the population level, with gradient forest models. Reported range shifts are species-specific and include both predicted range gains and losses. Forecasted species responses to climate change are strongly influenced by changes in a suite of environmental variables, from sea surface salinity and sea surface temperature, to minimum air temperature. Our results further suggest a mismatch between future habitat suitability (where species can remain in their ecological niche) and genomic vulnerability (where populations retain their genomic composition), highlighting the inter- and intraspecific variability in species' sensitivity to global change. Overall, this study demonstrates the importance of considering species and population level climatic vulnerability when proactively managing coastal marine ecosystems in the Anthropocene.

Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics

Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.

A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions

Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package.

Comparative phylogeography and palaeomodelling reveal idiosyncratic responses to climate changes in Neotropical paper wasps

The impact of the broad disjunction between Amazonia and the Atlantic Forest on biodiversity has been the theme of several discussions in recent decades. Here, we evaluate the effects of dependence on humid environments and the role of historical factors on the level, distribution and structuring of genetic variation in widely distributed Neotropical insects. For such, we test whether climatically stable zones (i.e. refuges) in both Amazonia and the Atlantic Forest concentrate higher genetic diversity in the social paper wasps Angiopolybia pallens and Synoeca surinama. We found that historical events have avoided the interchange of A. pallens between both rainforests at least since the Early Pliocene and that ancient colonization in north-western Amazonia and the Bahia refuge significantly predicts genetic diversity in populations of this species. Conversely, the split between the Atlantic Forest and remaining western populations of S. surinama is more recent (Plio-Pleistocene); this species has considerably lower genetic diversity than A. pallens and such diversity is mostly concentrated in Amazonia and in the cerrado biome (savanna) than in the Atlantic Forest. Finally, we propose that the occurrence of species that exhibit such distribution patterns should be taken into consideration when establishing areas for conservation.

Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics

We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. We generated spatial-temporal reconstructions using Bayesian inference in a coalescent framework in combination with hind-cast projections of species distribution models (SDMs). We also used the results and literature information to test alternative diversification scenarios via approximate Bayesian computation (ABC). Our results show that Quaternary climatic fluctuations influenced the geographic ranges of both species showing population expansion during the last glacial maximum (LGM) and range contraction during interglacial periods, as inferred from selected ABC models and from past projections of SDMs. We recovered Pleistocene diversification for both species occuring in distinctly unique periods for each taxon. An older and range-restricted lineage was recovered in a geographically isolated geological massif, deserving conservation and further taxonomic study. The diversification and distribution of these amphibian species endemic to the Neotropical 'campo rupestre' were influenced by Quaternary climatic fluctuations. The expansion of cold adapted species restricted to higher elevations during glacial periods and their concomitant retraction during interglacial periods may have been crucial for producing patterns of species richness and endemism along elevation gradients in tropical and subtropical domains. Such processes may influence the evolution of the biota distributed in heterogeneous landscapes with varied topography.

Population genomics for wildlife conservation and management

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata)

Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.

Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest

The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.

Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand

Phylogeographic concordance, or the sharing of phylogeographic patterns among codistributed species, suggests similar responses to topography or climatic history. While the orientation and timing of breaks between lineages are routinely compared, spatial dynamics within regions occupied by individual lineages provide a second opportunity for comparing responses to past events. In environments with complex topography and glacial history, such as New Zealand's South Island, geographically nested comparisons can identify the processes leading to phylogeographic concordance between and within regional genomic clusters. Here, we used single nucleotide polymorphisms (obtained via ddRADseq) for two codistributed forest beetle species, Agyrtodes labralis (Leiodidae) and Brachynopus scutellaris (Staphylinidae), to evaluate the role of climate change and topography in shaping phylogeographic concordance at two, nested spatial scales: do species diverge over the same geographic barriers, with similar divergence times? And within regions delimited by these breaks, do species share similar spatial dynamics of directional expansion or isolation-by-distance? We found greater congruence of phylogeographic breaks between regions divided by the strongest dispersal barriers (i.e., the Southern Alps). However, these shared breaks were not indicative of shared spatial dynamics within the regions they delimit, and the most similar spatial dynamics between species occurred within regions with the strongest gradients in historical climatic stability. Our results indicate that lack of concordance as traditionally detected by lineage turnover does not rule out the possibility of shared histories, and variation in the presence and type of concordance may provide insights into the different processes shaping phylogeographic patterns across geologically dynamic regions.

Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest

Comparative phylogeography is a powerful approach to investigate the role of historical and environmental processes in the evolution of biodiversity within a region. In this regard, comparative studies of species with similar habitat preferences are valuable to reduce the confounding influence of habitat association when interpreting phylogeographic patterns. In the Atlantic Forest of South America, phylogeographic studies of highland and lowland species have shown distinct population structure patterns so far, suggesting that such species have responded differently to Pleistocene glacial cycles. Herein, we performed a comparative analysis using molecular data and paleodistribution models of two Montane Atlantic Forest (MAF) co-distributed passerine birds with similar habitat requirements but with distinct life-history traits and ecologies: the frugivore lek-breeding Blue Manakin (Chiroxiphia caudata) and the insectivore and socially monogamous Drab-Breasted Bamboo Tyrant (Hemitriccus diops). We aimed to shed light on the role of contrasting life histories and ecologies onto the demography and population structure of MAF species. We sampled both species throughout most of their distribution range, sequenced a mitochondrial and a nuclear molecular marker, and used standard phylogeographic methods to investigate population structure and ecological niche modeling (ENM) to infer the species' paleodistributions. Our analyses recovered a phylogeographic break in H. diops in the region of the Doce River, but no genetic structure in C. caudata. We also found higher differentiation among subpopulations within each lineage of H. diops than among subpopulations of C. caudata. We suggest that these discrepancies in population structure might be due to distinct life-history traits and their impact on gene flow and generation time. For example, while H. diops is an insectivore species, C. caudata is a frugivore and the latter ecological aspect likely selects for a higher dispersion distance. Additionally, because C. caudata is a lek-breeding species, it has a longer generation time than H. diops. These traits could hinder genetic differentiation when populations become geographically isolated. Nonetheless, both species showed some common biological features, such as signatures of synchronous population expansion and larger distribution ranges during the Last Glacial Maximum, possibly due to similar cold tolerance.

Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (n= 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, Structure) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.

The combined role of dispersal and niche evolution in the diversification of Neotropical lizards

Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large-scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid-Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic-driven divergence at dynamic forest-savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.

Evolutionary genomics can improve prediction of species' responses to climate change

Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go extinct. Current approaches to predicting species responses to GCC begin to combine ecological and evolutionary information for species distribution modelling. Including an evolutionary dimension will substantially improve species distribution projections which have not accounted for key processes such as dispersal, adaptive genetic change, demography, or species interactions. However, eco-evolutionary models require new data and methods for the estimation of a species' adaptive potential, which have so far only been available for a small number of model species. To represent global biodiversity, we need to devise large-scale data collection strategies to define the ecology and evolutionary potential of a broad range of species, especially of keystone species of ecosystems. We also need standardized and replicable modelling approaches that integrate these new data to account for eco-evolutionary processes when predicting the impact of GCC on species' survival. Here, we discuss different genomic approaches that can be used to investigate and predict species responses to GCC. This can serve as guidance for researchers looking for the appropriate experimental setup for their particular system. We furthermore highlight future directions for moving forward in the field and allocating available resources more effectively, to implement mitigation measures before species go extinct and ecosystems lose important functions.

Pre-quaternary diversification and glacial demographic expansions of Cardiocrinum (Liliaceae) in temperate forest biomes of Sino-Japanese Floristic Region

The Sino-Japanese Floristic Region (SJFR) in East Asia is one of the most diverse temperate floras in the world. However, the relative influence of Neogene palaeogeographical changes and Quaternary climatic fluctuations as causal mechanisms on species diversification remains largely controversial, because most divergence time estimates were inferred from single-locus data and have limited geographic or taxonomic sampling. To evaluate these influences, we use SNP markers from restriction site-associated DNA sequencing (RAD-Seq) loci and expressed sequence tags-simple sequence repeat (EST-SSR) markers to investigate the levels of genetic variation, speciation and demographic history of the temperate-deciduous forest (TDF) endemic Cardiocrinum (Endlicher) Lindley (Liliaceae), a genus comprising three species in China (C. giganteum, C. cathayanum) and Japan (C. cordatum). Phylogenomic and population genomic coalescent-based analyses demonstrated that Late Neogene tectonic/climatic events triggered speciation of Cardiocrinum, and Pleistocene climatic fluctuations had limited influence on its divergence history. Population demographic inference using Approximate Bayesian Computation from EST-SSRs and palaeoclimatic niche models both indicated that all three Cardiocrinum species experienced population expansions during the transition from the LIG to the LGM. We also discussed the implications of these results on the conservation of montane TDF species in the SJFR under ongoing environmental change. Our results improve our understanding of how the constituents of montane TDF across the SJFR responded to previous periods of rapid climate and environmental change in terms of speciation and population demographic processes.

History and Geography of Neotropical Tree Diversity

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador's Yasuní Forest, which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests. We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.

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.

Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations

Environmental gradients constrain physiological performance and thus species' ranges, suggesting that species occurrence in diverse environments may be associated with local adaptation. Genome-environment association analyses (GEAA) have become central for studies of local adaptation, yet they are sensitive to the spatial orientation of historical range expansions relative to landscape gradients. To test whether potentially adaptive genotypes occur in varied climates in wide-ranged species, we implemented GEAA on the basis of genomewide data from the anole lizards Anolis ortonii and Anolis punctatus, which expanded from Amazonia, presently dominated by warm and wet settings, into the cooler and less rainy Atlantic Forest. To examine whether local adaptation has been constrained by population structure and history, we estimated effective population sizes, divergence times, and gene flow under a coalescent framework. In both species, divergence between Amazonian and Atlantic Forest populations dates back to the mid-Pleistocene, with subsequent gene flow. We recovered eleven candidate genes involved with metabolism, immunity, development, and cell signaling in A. punctatus and found no loci whose frequency is associated with environmental gradients in A. ortonii. Distinct signatures of adaptation between these species are not associated with historical constraints or distinct climatic space occupancies. Similar patterns of spatial structure between selected and neutral SNPs along the climatic gradient, as supported by patterns of genetic clustering in A. punctatus, may have led to conservative GEAA performance. This study illustrates how tests of local adaptation can benefit from knowledge about species histories to support hypothesis formulation, sampling design, and landscape gradient characterization.

Unraveling the influences of climate change in Lepidosauria (Reptilia)

In recent decades, changes in climate have caused impacts on natural and human systems on all continents and across the oceans and many species have shifted their geographic ranges, seasonal activities, migration patterns, abundances and interactions in response to these changes. Projections of future climate change are uncertain, but the Earth's warming is likely to exceed 4.8 °C by the end of 21th century. The vulnerability of a population, species, group or system due to climate change is a function of impact of the changes on the evaluated system (exposure and sensitivity) and adaptive capacity as a response to this impact, and the relationship between these elements will determine the degree of species vulnerability. Predicting the potential future risks to biodiversity caused by climate change has become an extremely active field of research, and several studies in the last two decades had focused on determining possible impacts of climate change on Lepidosaurians, at a global, regional and local level. Here we conducted a systematic review of published studies in order to seek to what extent the accumulated knowledge currently allow us to identify potential trends or patterns regarding climate change effects on lizards, snakes, amphisbaenians and tuatara. We conducted a literature search among online literature databases/catalogues and recorded 255 studies addressing the influence of climate change on a total of 1918 species among 49 Lepidosaurian's families. The first study addressing this subject is dated 1999. Most of the studies focused on species distribution, followed by thermal biology, reproductive biology, behavior and genetics. We concluded that an integrative approach including most of these characteristics and also bioclimatic and environmental variables, may lead to consistent and truly effective strategies for species conservation, aiming to buffer the climate change effects on this group of reptiles.

PaleoClim, high spatial resolution paleoclimate surfaces for global land areas

High-resolution, easily accessible paleoclimate data are essential for environmental, evolutionary, and ecological studies. The availability of bioclimatic layers derived from climatic simulations representing conditions of the Late Pleistocene and Holocene has revolutionized the study of species responses to Late Quaternary climate change. Yet, integrative studies of the impacts of climate change in the Early Pleistocene and Pliocene - periods in which recent speciation events are known to concentrate - have been hindered by the limited availability of downloadable, user-friendly climatic descriptors. Here we present PaleoClim, a free database of downscaled paleoclimate outputs at 2.5-minute resolution (~5 km at equator) that includes surface temperature and precipitation estimates from snapshot-style climate model simulations using HadCM3, a version of the UK Met Office Hadley Centre General Circulation Model. As of now, the database contains climatic data for three key time periods spanning from 3.3 to 0.787 million years ago: the Marine Isotope Stage 19 (MIS19) in the Pleistocene (~787 ka), the mid-Pliocene Warm Period (~3.264-3.025 Ma), and MIS M2 in the Late Pliocene (~3.3 Ma).

Using Genomic Data to Infer Historic Population Dynamics of Nonmodel Organisms

Genome sequence data are now being routinely obtained from many nonmodel organisms. These data contain a wealth of information about the demographic history of the populations from which they originate. Many sophisticated statistical inference procedures have been developed to infer the demographic history of populations from this type of genomic data. In this review, we discuss the different statistical methods available for inference of demography, providing an overview of the underlying theory and logic behind each approach. We also discuss the types of data required and the pros and cons of each method. We then discuss how these methods have been applied to a variety of nonmodel organisms. We conclude by presenting some recommendations for researchers looking to use genomic data to infer demographic history.

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences

Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (N_e ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. N_e curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in N_e differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.