Small body size increases the regional differentiation of populations of tropical mantellid frogs (Anura: Mantellidae)

Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species

The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well as other protected areas, is characterized by very species-rich and well-studied communities of animals and plants, but new species are still regularly discovered. Three species of phytotelmic frogs of the subgenus Pandanusicola in the genus Guibemantis are known from this area, G. flavobrunneus, G. liber, and G. pulcher. Further Pandanusicola frogs from this area have been provisionally assigned to G. bicalcaratus or G. albolineatus, pending detailed taxonomic review. During preliminary exploration of the ecology of these specialized frogs that live and reproduce in the leaf axils of Pandanus screw pines, we noticed the syntopic presence of two differently colored and differently sized Pandanusicola in Andasibe that could not be unambiguously assigned to any known species. A genetic screening revealed that these correspond to yet two further species in the area. Based on our data, seven species of Pandanusicola occur in Andasibe and nearby forests: (1) G. liber, the only non-phytotelmic species of the subgenus in the region; (2) G. flavobrunneus which is the largest species and characterized by a diagnostic yellowish brown dorsal pattern; (3) G. pulcher, characterized by translucent-green color with purplish brown spotting not observed in any other species in the area; (4) G. methueni, a brownish species usually lacking contrasted dorsolateral bands that differs from the other species in the area by emitting a characteristic trill-like advertisement call series (rather than clicks or chirps) and according to our data is widespread along Madagascars east coast; as well as three new species: (5) G. ambakoana sp. nov., a brownish species, typically with contrasted incomplete light dorsolateral bands and with single click-like advertisement calls; (6) G. vakoa sp. nov., a species that is equally brownish but lacks contrasted light dorsolateral bands and that has single click-like advertisement calls of very short duration; and (7) G. rianasoa sp. nov., a species that is smaller sized and has less distinct femoral glands than all the others, and emits a short series of soft chirp-like advertisement calls. All these species are genetically highly distinct, with >5% uncorrected pairwise distances in the mitochondrial 16S rRNA gene, and lack of haplotype sharing in two nuclear-encoded genes. The co-occurrence of seven Pandanusicola frogs in a relatively small geographic area is unprecedented in Madagascar and calls for in-depth studies of a possible differentiation in habitat use and life history.

Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles

Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.

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.

Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)

Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.

Unravelling the cryptic diversity and evolution of the dwarf swamp frog Pseudopaludicola mystacalis (Anura, Leptodactylidae) in open habitats of South America

Many studies on the diversity of the South American biota support the role of ecological and geological events as main drivers of species diversification. For many groups, geomorphological events are the key drivers of diversification, while the influence of Pleistocene climate oscillations is prominent for others. To precisely indicate which events were key for the development of the astonishing biodiversity in South America, studies on widely distributed species are paramount. One such species, the dwarf swamp frog Pseudopaludicola mystacalis (Leptodactylidae, Leiuperinae), is widely distributed in open habitats of South America and we herein investigate population differentiation and diversification in this species across its geographic range. We sequenced a 1374 bp mtDNA fragment from 64 specimens across 25 localities. We used population assignment and species delimitation methods to assess genetic structure and lineage limits across the species distribution. We estimated, for each lineage, intraspecific diversity, divergence times, and demographic histories. Our results recovered ten lineages with up to 5% of genetic divergence among them. Diversification occurred mainly during the Tertiary, suggesting that Miocene-Pliocene topographic events had a major influence on the diversification of P. mystacalis. Pleistocene climatic oscillations also played a role on evolutionary history of P. mystacalis, causing demographic changes in one lineage.

An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity

The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar's cryptic and microendemic amphibian diversity, yet they remain understudied. A new red-bellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffiakibomena known from Andasibe in the east. Stumpffialynnae sp. nov. adds another species to the red-bellied species complex, differing from S.kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6-3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as "Endangered". This species is the first Stumpffia described from Madagascar's central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type.

Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence

In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.

The Pristimantis trachyblepharis species group, a clade of miniaturized frogs: description of four new species and insights into the evolution of body size in the genus

Species richness in the genus Pristimantis is underestimated due to the existence of morphologically cryptic species. This is worsened by the low sampling effort and the lack of studies using genetic markers. Here, we use molecular and morphological data to determine the phylogenetic relationships of a clade of Pristimantis distributed throughout montane tropical forests in the eastern Andes, from central Ecuador to northern Perú. We name this clade the Pristimantis trachyblepharis species group. Our results show that it comprises nine species, of which four are formally described and five are new. Four of these undescribed species are formally described here. The group is composed of miniaturized species, such as Pristimantis nanus sp. nov., currently the smallest known species of the genus and the smallest vertebrate in Ecuador. As a first approach to understanding the evolutionary origin and implications of body-size reduction in Pristimantis, we here study the phylogenetic signal and evolutionary trends of body size within the genus. We also provide the first record of P. aquilonaris in Ecuador and we show, for the first time, the phylogenetic position of P. albujai, P. aquilonaris, P. minimus and P. trachyblepharis, which are also members of the P. trachyblepharis species group.

Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree-dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.

Gene Flow in Volant Vertebrates: Species Biology, Ecology and Climate Change

Gene flow, the exchange of genetic material between populations is an important biological process, which shapes and maintains biodiversity. The successful movement of individuals between populations depends on multiple factors determined by species biology and the environment. One of the most important factors regulating gene flow is the ability to move, and flight allows individuals to easily move across geographical barriers. Volant vertebrates are found on some of the remotest islands and contribute significantly to the biodiversity and ecosystem. The availability of next-generation sequencing data for non-model animals has substantially improved our understanding of gene flow and its consequences, allowing us to look at fine-scale patterns. However, most of our understanding regarding gene flow comes from the temperate regions and the Neotropics. The lack of studies from species-rich Asia is striking. In this review, we outline the importance of gene flow and the factors affecting gene flow, especially for volant vertebrates. We especially discuss research studies from tropical biomes of South and Southeast Asia, highlight the lacuna in literature and provide an outline for future studies in this species-rich region.

Evolutionary principles guiding amphibian conservation

The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.

Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot

The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.

Functional traits explain amphibian distribution in the Brazilian Atlantic Forest

AIM

Species distributions are one of the most important ways to understand how communities interact through macroecological relationships. The functional abilities of a species, such as its plasticity in various environments, can determine its distribution, species richness and beta diversity patterns. In this study, we evaluate how functional traits influence the distribution of amphibians, and hypothesize which functional traits explain the current pattern of amphibian species composition.

LOCATION

Atlantic Forest, Brazil.

TAXON

Amphibia (Anura and Gymnophiona).

METHODS

Using potential distributions of Brazilian amphibians from Atlantic Forest based on their functional traits, we analysed the influence of biotic and abiotic factors on species richness, endemism (with permutation multivariate analysis) and beta diversity components (i.e. total, turnover and nestedness dissimilarities).

RESULTS

Environmental variables explained 59.5% of species richness, whereas functional traits explained 15.8% of species distribution (geographical species range) for Anuran and 88.8% for Gymnophiona. Body size had the strongest correlation with species distribution. Results showed that species with medium to large body size, and species that are adapted to living in open areas tended to disperse from west to east direction. Current forest changes directly affected beta diversity patterns (i.e. most species adapted to novel environments increase their ranges). Beta diversity partitioning between humid and dry forests showed decreased nestedness and increased turnover by increasing altitude in the south-eastern region of the Atlantic Forest.

MAIN CONCLUSIONS

Our study shows that functional traits directly influence the ability of the species to disperse. With the alterations of the natural environment, species more apt to these alterations have dispersed or increased their distribution, which consequently changes community structure. As a result, there are nested species distribution patterns and homogenization of amphibian species composition throughout the Brazilian Atlantic Forest.

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.

Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella

Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.

Diversity of miniaturized frogs of the genus Adelophryne (Anura: Eleutherodactylidae): A new species from the Atlantic Forest of northeast Brazil

The number of species of frogs in the South American genus Adelophryne has increased in recent years, and it has become apparent that this group contains a substantial amount of undescribed diversity. Currently the genus contains nine described species and five candidate species. Here we describe the tenth species of the genus Adelophryne from the municipality of Igrapiúna, southern Bahia state, Brazil. The new species is characterized by its small body size, indistinct tympanum, and two phalanges in the finger IV. The species of the genus are distributed in three groups, Northern Amazonia Clade, Northern Atlantic Forest Clade and Southern Atlantic Forest Clade. The new species is phylogenetically related to species of the Northern Atlantic Forest Clade of Adelophryne and restricted to forested habitat, as typical for other Adelophryne. The species is restricted to the pristine forests in the type locality, and we consider its conservation status as Near Threatened. New morphological and molecular data of other Adelophryne species are presented, extending the distribution of Adelophryne sp. 2, Adelophryne sp. 4, Adelophryne mucronata and Adelophryne glandulata. However, a more comprehensive revision of the diversity and phylogenetic position of most Adelophryne species is needed, and the evolutionary relationships of A. meridionalis and A. pachydactyla remain unknown.

Syntopic frogs reveal different patterns of interaction with the landscape: A comparative landscape genetic study of Pelophylax nigromaculatus and Fejervarya limnocharis from central China

Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (F_ST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (F_ST′ = 0.401) than in PN (F_ST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes.

Habitat Association Predicts Genetic Diversity and Population Divergence in Amazonian Birds

The ecological traits of organisms may predict their genetic diversity and population genetic structure and mediate the action of evolutionary processes important for speciation and adaptation. Making these ecological-evolutionary links is difficult because it requires comparable genetic estimates from many species with differing ecologies. In Amazonian birds, habitat association is an important component of ecological diversity. Here, we examine the link between habitat association and genetic parameters using 20 pairs of closely related Amazonian bird species in which one member of the pair occurs primarily in forest edge and floodplains and the other occurs in upland forest interior. We use standardized geographic sampling and data from 2,416 genomic markers to estimate genetic diversity, population genetic structure, and statistics reflecting demographic and evolutionary processes. We find that species of upland forest have greater genetic diversity and divergence across the landscape as well as signatures of older histories and less gene flow than floodplain species. Our results reveal that species ecology in the form of habitat association is an important predictor of genetic diversity and population divergence and suggest that differences in diversity between floodplain and upland avifaunas in the Amazon may be driven by differences in the demographic and evolutionary processes at work in the two habitats.

How do rivers, geographic distance, and dispersal behavior influence genetic structure in two sympatric New World monkeys?

Dispersal, one of the major factors affecting the gene flow between populations, shapes the spatial distribution of genetic diversity within species. Alouatta macconnelli and Saguinus midas are two Neotropical monkey species that sympatrically inhabit the Guiana shield in northern Amazonia and are likely to differ in their dispersal behavior and vagility. We took advantage of their sympatry to investigate, over a fine geographical scale (∼50 km long), the relationship between spatial genetic structure, on the one hand, and geographical features and the species' dispersal behavior on the other. A total of 84 A. macconnelli individuals from 25 social units and 76 S. midas individuals from 19 social units were genotyped for nine microsatellite markers. Both species displayed high genetic diversity and allelic richness. However, patterns of genetic structure differed between the two species. In A. macconnelli, no genetic substructuring was observed, while in S. midas we detected significant structuring, but this structuring was not correlated with geographical features, such as the location of individuals relative to the river and/or the distance between them. Instead, the geographical distribution of genetic variation observed for each species is predominantly explained by each species' dispersal pattern. We identified bisexual dispersal for both species, but with significant differences, either in the distance or in the rate of dispersal, between species and sexes. Genetic relatedness within social units was higher in S. midas than in A. macconnelli: gene flow between social units seems limited in S. midas, especially for females, while high dispersal characterizes A. macconnelli, where females seem to disperse at lower rate but at a longer distance than males.

Diversification of the rainfrog Pristimantis ornatissimus in the lowlands and Andean foothills of Ecuador

Geographic barriers and elevational gradients have long been recognized as important in species diversification. Here, we illustrate an example where both mechanisms have shaped the genetic structure of the Neotropical rainfrog, Pristimantis ornatissimus, which has also resulted in speciation. This species was thought to be a single evolutionary lineage distributed throughout the Ecuadorian Chocó and the adjacent foothills of the Andes. Based on recent sampling of P. ornatissimus sensu lato, we provide molecular and morphological evidence that support the validity of a new species, which we name Pristimantis ecuadorensis sp. nov. The sister species are elevational replacements of each other; the distribution of Pristimantis ornatissimus sensu stricto is limited to the Ecuadorian Chocó ecoregion (< 1100 m), whereas the new species has only been found at Andean localities between 1450-1480 m. Given the results of the Multiple Matrix Regression with Randomization analysis, the genetic difference between P. ecuadorensis and P. ornatissimus is not explained by geographic distance nor environment, although environmental variables at a finer scale need to be tested. Therefore this speciation event might be the byproduct of stochastic historic extinction of connected populations or biogeographic events caused by barriers to dispersal such as rivers. Within P. ornatissimus sensu stricto, morphological patterns and genetic structure seem to be related to geographic isolation (e.g., rivers). Finally, we provide an updated phylogeny for the genus, including the new species, as well as other Ecuadorian Pristimantis.

Phylogenetic effective sample size

In this paper I address the question-how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

Spatial Biodiversity Patterns of Madagascar's Amphibians and Reptiles

Madagascar has become a model region for testing hypotheses of species diversification and biogeography, and many studies have focused on its diverse and highly endemic herpetofauna. Here we combine species distribution models of a near-complete set of species of reptiles and amphibians known from the island with body size data and a tabulation of herpetofaunal communities from field surveys, compiled up to 2008. Though taxonomic revisions and novel distributional records arose since compilation, we are confident that the data are appropriate for inferring and comparing biogeographic patterns among these groups of organisms. We observed species richness of both amphibians and reptiles was highest in the humid rainforest biome of eastern Madagascar, but reptiles also show areas of high richness in the dry and subarid western biomes. In several amphibian subclades, especially within the Mantellidae, species richness peaks in the central eastern geographic regions while in reptiles different subclades differ distinctly in their richness centers. A high proportion of clades and subclades of both amphibians and reptiles have a peak of local endemism in the topographically and bioclimatically diverse northern geographic regions. This northern area is roughly delimited by a diagonal spanning from 15.5°S on the east coast to ca. 15.0°S on the west coast. Amphibian diversity is highest at altitudes between 800–1200 m above sea-level whereas reptiles have their highest richness at low elevations, probably reflecting the comparatively large number of species specialized to the extended low-elevation areas in the dry and subarid biomes. We found that the range sizes of both amphibians and reptiles strongly correlated with body size, and differences between the two groups are explained by the larger body sizes of reptiles. However, snakes have larger range sizes than lizards which cannot be readily explained by their larger body sizes alone. Range filling, i.e., the amount of suitable habitat occupied by a species, is less expressed in amphibians than in reptiles, possibly reflecting their lower dispersal capacity. Taxonomic composition of communities assessed by field surveys is largely explained by bioclimatic regions, with communities from the dry and especially subarid biomes distinctly differing from humid and subhumid biomes.

High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America

Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.

Undiagnosed cryptic diversity in small, microendemic frogs (Leptolalax) from the Central Highlands of Vietnam

A major obstacle in prioritizing species or habitats for conservation is the degree of unrecognized diversity hidden within complexes of morphologically similar, "cryptic" species. Given that amphibians are one of the most threatened groups of organisms on the planet, our inability to diagnose their true diversity is likely to have significant conservation consequences. This is particularly true in areas undergoing rapid deforestation, such as Southeast Asia. The Southeast Asian genus Leptolalax is a group of small-bodied, morphologically conserved frogs that inhabit the forest-floor. We examined a particularly small-bodied and morphologically conserved subset, the Leptolalax applebyi group, using a combination of molecular, morphometric, and acoustic data to identify previously unknown diversity within. In order to predict the geographic distribution of the group, estimate the effects of habitat loss and assess the degree of habitat protection, we used our locality data to perform ecological niche modelling using MaxEnt. Molecular (mtDNA and nuDNA), acoustic and subtle morphometric differences revealed a significant underestimation of diversity in the L. applebyi group; at least two-thirds of the diversity may be unrecognised. Patterns of diversification and microendemism in the group appear driven by limited dispersal, likely due to their small body size, with several lineages restricted to watershed basins. The L. applebyi group is predicted to have historically occurred over a large area of the Central Highlands of Vietnam, a considerable portion of which has already been deforested. Less than a quarter of the remaining forest predicted to be suitable for the group falls within current protected areas. The predicted distribution of the L. applebyi group extends into unsurveyed watershed basins, each potentially containing unsampled diversity, some of which may have already been lost due to deforestation. Current estimates of amphibian diversity based on morphology alone are misleading, and accurate alpha taxonomy is essential to accurately prioritize conservation efforts.

DNA Barcoding Survey of Anurans across the Eastern Cordillera of Colombia and the Impact of the Andes on Cryptic Diversity

Colombia hosts the second highest amphibian species diversity on Earth, yet its fauna remains poorly studied, especially using molecular genetic techniques. We present the results of the first wide-scale DNA barcoding survey of anurans of Colombia, focusing on a transect across the Eastern Cordillera. We surveyed 10 sites between the Magdalena Valley to the west and the eastern foothills of the Eastern Cordillera, sequencing portions of the mitochondrial 16S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) genes for 235 individuals from 52 nominal species. We applied two barcode algorithms, Automatic Barcode Gap Discovery and Refined Single Linkage Analysis, to estimate the number of clusters or “unconfirmed candidate species” supported by DNA barcode data. Our survey included ~7% of the anuran species known from Colombia. While barcoding algorithms differed slightly in the number of clusters identified, between three and ten nominal species may be obscuring candidate species (in some cases, more than one cryptic species per nominal species). Our data suggest that the high elevations of the Eastern Cordillera and the low elevations of the Chicamocha canyon acted as geographic barriers in at least seven nominal species, promoting strong genetic divergences between populations associated with the Eastern Cordillera.

Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs

The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this biodiversity hotspot. Both extrinsic and intrinsic factors have been studied in a comparative framework, with extrinsic factors usually being related to the physical environment (landscape, climate, river catchments, mountain chains), and intrinsic factors being clade-specific traits or constraints (reproduction, ecology, morphology, physiology). Despite some general patterns emerging from such large-scale comparative analyses, it became clear that the mechanism of diversification in Madagascar may vary among clades, and may be a multifactorial process. In this contribution, I test for intrinsic factors promoting population-level divergence within a clade of terrestrial, diurnal leaf-litter frogs (genus Gephyromantis) that has previously been shown to diversify according to extrinsic factors. Landscape genetic analyses of the microendemic species Gephyromantis enki and its widely distributed, larger sister species Gephyromantis boulengeri over a rugged landscape in the Ranomafana area shows that genetic variance of the smaller species cannot be explained by landscape resistance alone. Both topographic and riverine barriers are found to be important in generating this divergence. This case study yields additional evidence for the probable importance of body size in lineage diversification.

High levels of diversity uncovered in a widespread nominal taxon: continental phylogeography of the neotropical tree frog Dendropsophus minutus

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km². One of them occupies an area of almost one million km² encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

A multi-clade test supports the intermediate dispersal model of biogeography

BACKGROUND

Biogeography models typically focus on explaining patterns through island properties, such as size, complexity, age, and isolation. Such models explain variation in the richness of island biotas. Properties of the organisms themselves, such as their size, age, and dispersal abilities, in turn may explain which organisms come to occupy, and diversify across island archipelagos. Here, we restate and test the intermediate dispersal model (IDM) predicting peak diversity in clades of relatively intermediate dispersers.

METHODOLOGY

We test the model through a review of terrestrial and freshwater organisms in the western Indian Ocean examining the correlation among species richness and three potential explanatory variables: dispersal ability quantified as the number of estimated dispersal events, average body size for animals, and clade age.

CONCLUSIONS

Our study supports the IDM with dispersal ability being the best predictor of regional diversity among the explored variables. We find a weaker relationship between diversity and clade age, but not body size. Principally, we find that richness strongly and positively correlates with dispersal ability in poor to good dispersers while a prior study found a strong decrease in richness with increased dispersal ability among excellent dispersers. Both studies therefore support the intermediate dispersal model, especially when considered together. We note that many additional variables not here considered are at play. For example, some taxa may lose dispersal ability subsequent to island colonization and some poor dispersers have reached high diversity through within island radiations. Nevertheless, our findings highlight the fundamental importance of dispersal ability in explaining patterns of biodiversity generation across islands.

Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

Genetic diversity, phylogeny and evolution of alkaloid sequestering in Cuban miniaturized frogs of the Eleutherodactylus limbatus group

The miniaturized frogs of the Eleutherodactylus limbatus group, endemic to Cuba, have recently been shown to contain alkaloids in their skin, representing the fifth independent evolutionary origin of alkaloid sequestering in anurans. Based on a comprehensive sampling of all known species of the group we here assess their range-wide phylogeography using DNA sequences of the mitochondrial cytochrome b and the nuclear Rag-1 gene. We found E. etheridgei, E. cubanus, and E. orientalis to be genetically highly distinct, with uncorrected pair-wise distances >12% in the cytochrome b gene and >5% in the 16S rRNA gene, and without haplotype sharing in the Rag-1 gene. On the contrary, E. iberia, E. jaumei, E. limbatus, and one unnamed lineage from Gran Piedra mountains had lower mitochondrial divergences to each other (<6% in cytochrome b; <3% in 16S) and extensive Rag-1 haplotype sharing, suggesting that their species status requires careful revision. All species and lineages of the group occur in the mountain areas of eastern Cuba and only one of them, E. limbatus, colonized central and western Cuba. Populations of this latter lineage are only weakly genetically differentiated, and its range expansion to western Cuba is probably Pleistocenic, demonstrating that also miniaturized frog species are able of considerable range expansions (over hundreds of kilometers) in short time spans. A phylogeny based on about 5 kb of mitochondrial and nuclear genes places, with maximum support, E. etheridgei basalmost in the group, followed by E. cubanus, E. orientalis, and the E. iberia-jaumei-limbatus clade. The screening of skin alkaloids revealed the presence of alkaloids in all lineages of the group, but alkaloids known to be sequestered by other anurans were not found in the basalmost E. etheridgei. Furthermore, individuals of the derived lineages of the E. iberia-jaumei-limbatus clade had a much larger variety of different alkaloid compounds (3-18) than the other three species (0-4). Traces of alkaloids were found in other species only remotely related to the E. limbatus group, i.e., E. caspari, E. goini, E. ricordii, and E. tetajulia. According to these findings, it can be hypothesized that the capacity to sequester dietary alkaloids into the skin evolved first in an ancestral, litter-dwelling and small-sized Cuban Eleutherodactylus, followed by evolution of miniaturization and diurnality in the early representatives of the E. limbatus group, and eventually by increased brightness of color with probable aposematic function and a highly efficient mechanism of alkaloid sequestering.

Fine-scale habitat associations of a terrestrial salamander: the role of environmental gradients and implications for population dynamics

Environmental gradients are instrumental in shaping the distribution and local abundance of species because at the most fundamental level, an organism’s performance is constrained by the environment it inhabits. In topographically complex landscapes, slope, aspect, and vegetative cover interact to affect solar exposure, creating temperature-moisture gradients and unique microclimates. The significance of the interaction of abiotic gradients and biotic factors such as competition, movement, or physiology has long been recognized, but the scale at which these factors vary on the landscape has generally precluded their inclusion in spatial abundance models. We used fine-scale spatial data relating to surface-soil moisture, temperature, and canopy cover to describe the spatial distribution of abundance of a terrestrial salamander, Plethodon albagula, across the landscape. Abundance was greatest in dense-canopy ravine habitats with high moisture and low solar exposure, resulting in a patchy distribution of abundance. We hypothesize that these patterns reflect the physiological constraints of Plethodontid salamanders. Furthermore, demographic cohorts were not uniformly distributed among occupied plots on the landscape. The probability of gravid female occurrence was nearly uniform among occupied plots, but juveniles were much more likely to occur on plots with lower surface temperatures. The disconnect between reproductive effort and recruitment suggests that survival differs across the landscape and that local population dynamics vary spatially. Our study demonstrates a connection between abundance, fine-scale environmental gradients, and population dynamics, providing a foundation for future research concerning movement, population connectivity, and physiology.

Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana

We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.