Revisiting the vanishing refuge model of diversification

Different approaches to understanding methodological adequacy in ecophysiological studies on small ectotherms

Body temperature (Tb) variation and environmental temperature gradients are more intense in small individuals because their body size allows for a more intimate relationship between Tb and the environment. To contribute to a methodological consensus on the ecophysiology of small ectotherms, we aimed to investigate whether different approaches and methodological techniques affect the measurement of critical temperatures in a small lizard (Coleodactylus meridionalis, Sphaerodactylidae) from the Atlantic Forest of southern Bahia, Brazil, and subsequently its vulnerability assessment. We measured two metrics of thermal physiology: critical thermal minimum (CTmin) and critical thermal maximum (CTmax). In total, four types of temperature measurements (protocols) were defined. In the first protocol, we estimated CTmax/CTmin without heating/cooling rate by directly measuring the lizard's midbody temperature. In the other three protocols, we used a ramping assay with a heating/cooling rate to estimate CTmax/CTmin in the chamber (height: 11.3 cm), substrate, and Tb of the lizard, respectively. In total 116 individuals of Coleodactylus meridionalis were collected, of which 177 CTmax and 131 CTmin were performed. C. meridionalis showed a mean CTmax of 41 °C and a mean CTmin of 8.9 °C when considering the Tb protocol, which is intermediate compared to the other protocols. The substrate temperature protocol was the closest to Tb, and for this, the best method for the small lizards using an infrared thermometer.

Geoclimatic drivers of diversification in the largest arid and semi-arid environment of the Neotropics: Perspectives from phylogeography

The South American Dry Diagonal, also called the Diagonal of Open Formations, is a large region of seasonally dry vegetation extending from northeastern Brazil to northern Argentina, comprising the Caatinga, Cerrado, and Chaco subregions. A growing body of phylogeography literature has determined that a complex history of climatic changes coupled with more ancient geological events has produced a diverse and endemic-rich Dry Diagonal biota. However, the exact drivers are still under investigation, and their relative strengths and effects are controversial. Pleistocene climatic fluctuations structured lineages via vegetation shifts, refugium formation, and corridors between the Amazon and Atlantic forests. In some taxa, older geological events, such as the reconfiguration of the São Francisco River, uplift of the Central Brazilian Plateau, or the Miocene inundation of the Chaco by marine incursions, were more important. Here, we review the Dry Diagonal phylogeography literature, discussing each hypothesized driver of diversification and assessing degree of support. Few studies statistically test these hypotheses, with most support drawn from associating encountered phylogeographic patterns such as population structure with the timing of ancient geoclimatic events. Across statistical studies, most hypotheses are well supported, with the exception of the Pleistocene Arc Hypothesis. However, taxonomic and regional biases persist, such as a proportional overabundance of herpetofauna studies, and the under-representation of Chaco studies. Overall, both Pleistocene climate change and Neogene geological events shaped the evolution of the Dry Diagonal biota, though the precise effects are regionally and taxonomically varied. We encourage further use of model-based analyses to test evolutionary scenarios, as well as interdisciplinary collaborations to progress the field beyond its current focus on the traditional set of geoclimatic hypotheses.

Speciation-by-Extinction

Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.

Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar

How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470-1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important.

Natural history predicts patterns of thermal vulnerability in amphibians from the Atlantic Rainforest of Brazil

In the Brazilian Atlantic Rainforest (AF), amphibians (625 species) face habitat degradation leading to stressful thermal conditions that constrain animal activity (e.g., foraging and reproduction). Data on thermal ecology for these species are still scarce. We tested the hypothesis that environmental occupation affects the thermal tolerance of amphibian species more than their phylogenetic relationships. We evaluated patterns of thermal tolerance of 47 amphibian species by assessing critical thermal maxima and warming tolerances, relating these variables with ecological covariates (e.g., adult macro- and microhabitat and site of larval development). We used mean and maximum environmental temperature, ecological covariates, and morphological measurements in the phylogenetic generalized least squares model selection to evaluate which traits better predict thermal tolerance. We did not recover phylogenetic signal under a Brownian model; our results point to a strong association between critical thermal maxima and habitat and development site. Forest species were less tolerant to warm temperatures than open area or generalist species. Species with larvae that develop in lentic environment were more tolerant than those in lotic ones. Thus, species inhabiting forest microclimates are more vulnerable to the synergistic effect of habitat loss and climate change. We use radar charts as a quick evaluation tool for thermal risk diagnoses using aspects of natural history as axes.

A new species of tree hyrax (Procaviidae: Dendrohyrax) from West Africa and the significance of the Niger–Volta interfluvium in mammalian biogeography

Tree hyraxes (Dendrohyrax) are one of only three genera currently recognized in Procaviidae, the only extant family in the mammalian order Hyracoidea. Their taxonomy and natural history have received little attention in recent decades. All tree hyrax populations of Guineo-Congolian forests of Africa are currently treated as a single species, Dendrohyrax dorsalis, the western tree hyrax, but many other groups of mammals distributed across this large biome have been shown to consist of several different species, each restricted to a distinct biogeographical region. We analysed variation in loud-call structure, pelage colour, skull morphometrics and mitochondrial genomes in populations across much of the range of D. dorsalis. This integrative approach uncovered considerable cryptic variation. The population found between the Niger and Volta Rivers in West Africa is particularly distinctive, and we describe it herein as a new species. Our study highlights the need to revise the taxonomy of the genus Dendrohyrax in light of modern systematics and current understanding of its distribution. It also adds to a growing body of evidence that the Niger–Volta interfluvium has a distinct meso-mammal fauna. Unfortunately, the fauna of this region is under major threat and warrants much greater conservation attention.

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.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

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.

Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves: Thamnophilidae)

In order to gain insights into the biogeographic processes underlying biotic diversification in the Atlantic Forest (AF), we used a multi-locus approach to examine the evolutionary history of the White-shouldered Fire-eye (Pyriglena leucoptera) and the Fringe-backed Fire-eye (Pyriglena atra), two parapatric sister species endemic to the AF. We sequenced one mitochondrial, three Z chromosome-linked and three anonymous markers of 556 individuals from 66 localities. We recovered four lineages throughout the AF: P. atra and three populations within P. leucoptera. All populations diverged during the late Pleistocene and presented varying levels of admixture. One Z-linked locus showed the highest level of differentiation between the two species. On the other hand, a mitochondrial haplotype was shared extensively between them. Our data supported vicariance driving speciation along with extinction and dispersal as processes underlying intraspecific diversification. Furthermore, signatures of demographic expansion in most populations and areas of genetic admixture were recovered throughout the AF, suggesting that forest fragmentation was also important in differentiation. Genetic admixture areas are located between large rivers suggesting that AF rivers may diminish gene flow. Our results indicated a complex and dynamic biogeographic history of Pyriglena in the AF, with vicariance, extinction, dispersal and secondary contact followed by introgression likely influencing the current patterns of genetic distribution.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Skull shape variation in extant pangolins (Pholidota: Manidae): allometric patterns and systematic implications

Pangolins are among the most endangered groups of mammals, comprising eight extant species delineated into three genera. Despite several studies dedicated to their skeletal anatomy, the potential taxonomic insight from cranial morphological variation in extant Pholidota is yet to be assessed with modern geometric morphometric methods. We present the first comprehensive study on the cranial morphology of extant pangolins and discuss its implications for the taxonomy and evolution of the group. We performed landmark-based morphometric analyses on 241 museum specimens to describe the variation in skull shape in seven of the eight extant species. Our analyses revealed genus- and species-level morphological discrimination, with Asian species (Manis spp.) being grouped together, whereas African pangolins present distinct skull shapes between small (Phataginus spp.) and large (Smutsia spp.) species. Analyses of allometry also identified a set of traits whose allometric trajectories distinguish Asian from African specimens. Finally, we uncovered intraspecific variation in skull shape in white-bellied pangolins (Phataginus tricuspis) that partly corroborates recent DNA-based differentiation among biogeographically distinct populations. Overall, our results shed light on the morphological diversity of the skull of these enigmatic myrmecophagous mammals and confirm the genus-level classification and cryptic diversity within the white-bellied pangolin revealed by molecular phylogenetics.

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.

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.

Speciation through the lens of biomechanics: locomotion, prey capture and reproductive isolation

Speciation is a multifaceted process that involves numerous aspects of the biological sciences and occurs for multiple reasons. Ecology plays a major role, including both abiotic and biotic factors. Whether populations experience similar or divergent ecological environments, they often adapt to local conditions through divergence in biomechanical traits. We investigate the role of biomechanics in speciation using fish predator-prey interactions, a primary driver of fitness for both predators and prey. We highlight specific groups of fishes, or specific species, that have been particularly valuable for understanding these dynamic interactions and offer the best opportunities for future studies that link genetic architecture to biomechanics and reproductive isolation (RI). In addition to emphasizing the key biomechanical techniques that will be instrumental, we also propose that the movement towards linking biomechanics and speciation will include (i) establishing the genetic basis of biomechanical traits, (ii) testing whether similar and divergent selection lead to biomechanical divergence, and (iii) testing whether/how biomechanical traits affect RI. Future investigations that examine speciation through the lens of biomechanics will propel our understanding of this key process.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.

Molecular data reveal spatial and temporal patterns of diversification and a cryptic new species of lowland Stenocercus Duméril & Bibron, 1837 (Squamata: Tropiduridae)

Phylogenetic studies have uncovered biogeographic patterns and the associated diversification processes of Neotropical wet forest taxa, yet the extensive open and drier biomes have received much less attention. In the Stenocercus lizard radiation, restricted sampling and phylogenetic information have limited inferences about the timing, spatial context, and environmental drivers of diversification in the open and dry lowland settings of eastern and southern South America. Based on new DNA sequence data of previously unsampled species, we provide an updated historical biogeographic hypothesis of Stenocercus. We infer phylogenetic relationships, estimate divergence times, and track ancestral distributions, asking whether cladogenetic events within the genus correlate to reported shifts in South American landscapes during the past 30millionyears, focusing in the open and drier areas. To examine correlations between genetic and ecological divergence, we extracted environmental data from occurrence records and estimated climatic envelopes occupied by lowland taxa. Our results suggest that Stenocercus began to diversify around the South American Midwest by the late Oligocene. We recovered two main lowland and two main Andean clades within the genus; within both Andean clades, most cladogenetic events date back to the Miocene, synchronously with the most intense phase of Andean uplift. In the western clade of lowland Stenocercus, species ranges and divergence times are consistent with major landscape shifts at the upper Guaporé and Paraguay River basins as a result of Andean orogeny, suggesting vicariant speciation. By contrast, in the 'horned' lowland clade, we find evidence that dispersal and ecological differentiation have shaped species divergences and current ranges in the Brazilian Cerrado, Caatinga, Pampas and Atlantic Forest, possibly under a vanishing refuge scenario. Lastly, our phylogenetic results indicate two divergent clades within the formerly recognized taxon S. sinesaccus, and further evaluation of morphological data corroborates the existence of a distinct, new species of Stenocercus, here described. The new taxon occurs in the Chapada dos Parecis massif in the Brazilian states of Mato Grosso and Rondônia.