The endotrophic nidicolous tadpole of Cycloramphus eleutherodactylus(Miranda-Ribeiro) (Anura: Cycloramphidae).

Cycloramphus Tschudi is the most speciose genus in the family Cycloramphidae, including 30 species endemic to the Atlantic forest Domain in Brazil (Frost 2022). Species in the genus may be classified as saxicolous and terrestrial based on morphology and reproductive mode. Saxicolous are flat-bodied species, with granular skin, and interdigital web (Heyer 1983a), associated with fast-flowing streams in all life history phases. They lay eggs over humid rocks, logs, or crevices in the splash zone, from which semiterrestrial tadpoles hatch (McDiarmid & Altig 1999; Dias et al. 2021) that feed over humid rocks inside the stream or dripping rocky walls (Lutz 1929; Heyer 1983a, b; Haddad & Sazima 1989; Giaretta & Cardoso 1995; Giaretta & Facure 2003; Lima et al. 2010). The single exception to this pattern is C. bandeirensis Heyer 1983a, which share the morphology of adults and larvae, but lives terrestrially, away from streams, in the rocky fields of open high elevation grasslands of Caparaó National Park (Verdade et al. 2019).

Two new species of geckos of the genus Phyllopezus Peters, 1878 (Squamata: Gekkota: Phyllodactylidae) from northeastern Brazil.

We describe two new species of Brazilian geckos of the genus Phyllopezus based on morphological and molecular data. The first species is currently known from a relictual Cerrado enclavecampos rupestres, in the mountains of the Serra do Espinhao in the state of Bahia. The second species is known from northeastern Atlantic Forest and transitional areas with Caatinga biome in the state of Alagoas. The two new species are sister taxa and together are the sister clade to the remaining species in the Phyllopezus pollicaris species complex. These new species can be morphologically distinguished from their congeners by meristic and morphometric characters, in addition to color pattern and genetic differentiation.

Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae).

The genus Pipa is a species-poor clade of Neotropical frogs and one of the most bizarre-looking due to many highly derived anatomical traits related to their fully aquatic lifestyle. With their African relatives, they form the Pipidae family, which has attracted much attention, especially regarding its anatomy, reproductive biology, paleontology and biogeography. However, the actual diversity and phylogenetic relationships within Pipa remain poorly understood, and thus so do their historical biogeography and the evolution of striking features, such as the absence of teeth and endotrophy in some species. Using short mtDNA sequences across the distribution of the genus, we identified 15 main lineages (Operational Taxonomic Units - OTUs). This more than doubles the number of the currently seven valid nominal species. Several closely related OTUs do not share nuDNA alleles, confirming species divergence. Time-calibrated phylogenies obtained from mitogenomes and from 10 nuclear loci provide highly similar topologies but strikingly distinct node ages for Pipa. High dN/dS ratios and the variation of substitution rates across the trees suggest a strong effect of saturation on fast evolving positions of mtDNA, producing a substantially shorter stem branch of Pipa. Focusing on the nuDNA topology, we inferred an early Neogene Amazonian origin of the diversification of Pipa, with an initial split between the Guiana-Brazilian Shields and Western Amazonia, a pattern observed in many other co-distributed groups. All the western species are edentate, suggesting a single loss in the genus. Each of these groups diversified further out of Amazonia, toward the Atlantic Forest and toward trans-Andean forests, respectively. These events are concomitant with paleogeographic changes and match patterns observed in other co-distributed taxonomic groups. The two Amazonian lineages have probably independently acquired endotrophic larval development.

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 new Chiasmocleis (Anura: Microhylidae) from the eastern Guiana Shield with an amended definition of C. haddadi Peloso, Sturaro, Forlani, Gaucher, Motta, & Wheeler, 2014.

The existence of an unnamed (candidate) species from French Guiana and the state of Amapá (Brazil) closely related to Chiasmocleis haddadi has been hypothesized in previous DNA-based studies. With an integrative use of genetic, morphological and acoustic data we confirm that these populations are indeed distinct from C. haddadi and all other known congeners. We herein describe and name this new species, and amend the definition of C. haddadi since the type-series and its original diagnosis included specimens of the new species. Geographically, the new species occurs eastward of its sister species C. haddadi from which it can be distinguished by having a larger body, a proportionally smaller eye and a distinct dorsal colouration. We suspect that the new species breeds in the leaf litter and that tadpoles undergo endotrophic development whereas co-occurring C. haddadi and C. hudsoni lay clutches in the leaf litter nearby standing water of temporary ponds where exotrophic tadpoles complete their development. This new species is a new addition to the already long list of animals being endemic to the easternmost part of the Guiana Shield, a region identified as a singular bioregion within Amazonia by previous research.

Revealing the cryptic diversity of the widespread and poorly known South American blind snake genus Amerotyphlops (Typhlopidae: Scolecophidia) through integrative taxonomy

Morphological stasis is generally associated with relative constancy in ecological pressures throughout time, producing strong stabilizing selection that retains similar shared morphology. Although climate and vegetation are commonly the main key factors driving diversity and phenotypic diversification in terrestrial vertebrates, fossorial organisms have their morphology mostly defined by their fossorial lifestyle. Among these secretive fossorial organisms, blind snakes of the South American genus Amerotyphlops are considered poorly studied when compared to other taxa. Here, we evaluate the cryptic diversity of Amerotyphlops using phylogenetic and multivariate approaches. We based our phylogenetic analysis on a molecular dataset composed of 12 gene fragments (eight nuclear and four mitochondrial) for 109 species of Typhlopidae. The multivariate analysis was implemented using 36 morphological variables for 377 specimens of Amerotyphlops. Additionally, we contrast our phylogenetic result with the morphological variation found in cranial, external and hemipenial traits. Our phylogenetic results recovered with strong support the following monophyletic groups within Amerotyphlops: (1) a clade formed by A. tasymicris and A. minuisquamus; (2) a clade composed of A. reticulatus; (3) a north-eastern Brazilian clade including A. yonenagae, A. arenensis, A. paucisquamus and A. amoipira; and (4) a clade composed of A. brongersmianus and a complex of cryptic species. Based on these results we describe four new species of Amerotyphlops from north-eastern and south-eastern Brazil, which can be distinguished from the morphologically similar species, A. brongersmianus and A. arenensis.

Reassessing the systematics of Leptodeira (Serpentes, Dipsadidae) with emphasis in the South American species

Within the diverse subfamily Dipsadinae, Imantodini represents one of the few groups distributed in North, Central and South America. The tribe comprises the genera Leptodeira and Imantodes, from which Leptodeira is the most diverse, including 15 species and 11 subspecies, distributed from southern USA to central Argentina. Taxonomy and affinities among these taxa are poorly resolved, and the phylogenetic relationships among the South American diversity were never properly assessed before. Here, we investigate the phylogenetic relationships and the taxonomic status of Leptodeira spp. based on a comprehensive multilocus dataset with emphasis in the South American radiation. Besides assessing the phylogenetic relationship and species cohesion, we also evaluate the morphological variation among the South American diversity of Leptodeira. Our results support the monophyly of Imatodini and Leptodeira, while indicating that several individuals classified as Leptodeira annulata and L. septentrionalis do not cluster together within their respective species. Moreover, specimens identified as belonging to the subspecies L. a. annulata, L. a. cussiliris, L. s. ornata and L. s. polysticta do not group together suggesting the current classification includes non-natural groups. The analysis of morphological evidence also supports the phylogenetics results, indicating that several clades can be recognized as evolutionary units presenting distinct phenotypes. To equate the taxonomy to our results, we propose a new taxonomic arrangement for Leptodeira in which we are: (1) redefining the composition of L. annulata and L. septentrionalis; (2) elevating five subspecies to species level; (3) revalidating one species; (4) recognizing four species complexes; and (5) indicating the presence of hidden diversity (probably four undescribed species). Finally, we describe a new species (Leptodeira tarairiu sp. nov.) from the open formations of South America (Cerrado and Caatinga), and we provide detailed redescriptions for all South American species of Leptodeira.

Evolutionary drivers of sexual signal variation in Amazon Slender Anoles.

Phenotypic variation among populations, as seen in the signaling traits of many species, provides an opportunity to test whether similar factors generate repeated phenotypic patterns in different parts of a species' range. We investigated whether genetic divergence, abiotic gradients, and sympatry with closely related species explain variation in the dewlap colors of Amazon Slender Anoles, Anolis fuscoauratus. To this aim, we characterized dewlap diversity in the field with respect to population genetic structure and evolutionary relationships, assessed whether dewlap phenotypes are associated with climate or landscape variables, and tested for nonrandom associations in the distributions of A. fuscoauratus phenotypes and sympatric Anolis species. We found that dewlap colors vary among but not within sites in A. fuscoauratus. Regional genetic clusters included multiple phenotypes, while populations with similar dewlaps were often distantly related. Phenotypes did not segregate in environmental space, providing no support for optimized signal transmission at a local scale. Instead, we found a negative association between certain phenotypes and sympatric Anolis species with similar dewlap color attributes, suggesting that interactions with closely related species promoted dewlap divergence among A. fuscoauratus populations. Amazon Slender Anoles emerge as a promising system to address questions about parallel trait evolution and the contribution of signaling traits to speciation.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males.

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group).

General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.

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.

Male-male competition and repeated evolution of terrestrial breeding in Atlantic Coastal Forest frogs.

Terrestrial breeding is a derived condition in frogs, with multiple transitions from an aquatic ancestor. Shifts in reproductive mode often involve changes in habitat use, and these are typically associated with diversification in body plans, with repeated transitions imposing similar selective pressures. We examine the diversification of reproductive modes, male and female body sizes, and sexual size dimorphism (SSD) in the Neotropical frog genera Cycloramphus and Zachaenus, both endemic to the Atlantic rainforest of Brazil. Species in this clade either breed in rocky streams (saxicolous) or in terrestrial environments, allowing us to investigate reproductive habitat shifts. We constructed a multilocus molecular phylogeny and inferred evolutionary histories of reproductive habitats, body sizes, and SSD. The common ancestor was small, saxicolous, and had low SSD. Terrestrial breeding evolved independently three times and we found a significant association between reproductive habitat and SSD, with shifts to terrestrial breeding evolving in correlation with decreases in male body size, but not female body size. Terrestrial breeding increases the availability of breeding sites and results in concealment of amplexus, egg-laying, and parental care, therefore reducing male-male competition at all stages of reproduction. We conclude that correlated evolution of terrestrial reproduction and small males is due to release from intense male-male competition that is typical of exposed saxicolous breeding.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

Rain forest shifts through time and riverine barriers shaped the diversification of South American terrestrial pit vipers (Bothrops jararacussu species group)

Aim To investigate (a) historical biogeographical connections and species interchange among rain forest habitats and (b) the role of riverine barriers on population divergence and speciation in the Neotropical region. Location Amazonia and Atlantic Forest in South America. Taxon Bothrops jararacussu species group (Serpentes: Viperidae). Methods We inferred phylogenetic relationships within Bothrops with an emphasis on the jararacussu species group under a Bayesian framework based on six molecular loci. We also used genetic coalescent simulations and approximate Bayesian computation to infer historical demography within the jararacussu group based on tests of alternative scenarios. Results We found the jararacussu species group to be monophyletic. The Atlantic Forest species B. pirajai and B. muriciensis were inferred nested within this group, closely related to B. jararacussu, confirming that Atlantic Forest species form a clade. The historical demographic analyses support vicariant separation between populations of B. brazili north and south of the Amazon River during the Miocene–Pliocene border, as well as colonization of the Atlantic Forest by a northern Amazonian ancestor in the Pleistocene. Main Conclusion The evolutionary history of the jararacussu species group sheds light on the dynamism of Neotropical rain forests over time, with at least one event of forest expansion leading to faunal interchange between Amazonian and Atlantic forests in the Pleistocene. Moreover, tests of alternative demographic scenarios suggest that the populations of B. brazili from north and south of the Amazon River originated from a vicariant event during the Miocene–Pliocene border, in agreement with the proposed age of establishment of the modern Amazon River drainage. Our results also have taxonomic implications for these medically important venomous snakes, supporting unrecognized diversity at the species level.

Anurans of the Caparaó National Park and surroundings, southeast Brazil / Anuros do Parque Nacional do Caparaó e arredores, sudeste brasileiro

Abstract The Atlantic Forest (AF) is one of the biodiversity hotspots of the world, and the most fragmented biome of Brazil. This biome includes different phytophysiognomies, as riparian, slope, cloudy forests, and grasslands. Such complexity, allied to huge latitudinal and high elevational range, provides diverse habitats and conditions for amphibian speciation. As a result, there are over 600 amphibian species known to occur in the AF. Within this biome the Caparaó National Park (CNP) is relevant, as it includes the highest peak of the biome, the Pico da Bandeira at almost 3,000 m above sea level, as well as different phytophysiognomies as rocky fields and humid forests. In spite of that, its amphibian fauna is still poorly described. We inventoried amphibians at the CNP and surrounding areas from 2016 to 2018 and recorded 47 anuran species, of which two are locally endemic and at least six have not been described yet. Additionally, we compiled data from previous surveys (2004 to 2008) and secondary data from scientific collections. All together, we registered a total of 61 anuran species from 12 families for the CNP and surroundings, placing this area among the 10 amphibian richest sites in the AF. Some of these species are represented by only one or two collected specimens and have not been registered in the CNP since the 1980's, such as Thoropa lutzi and Hylodes vanzolinii. These species could be examples of population declines or even past local extinctions, highlighting the need of further sampling efforts in that highly biodiverse site.

Resumo A Mata Atlântica (MA) é considerada um dos hotspots de biodiversidade do mundo, sendo o bioma mais degradado no Brasil. Este bioma compreende muitas fitofisionomias, como floresta ombrófila, semidecidual, e campos de altitude. Esta complexidade, aliada à enorme variação latitudinal e altitudinal, disponibiliza habitats e condições diversas à especiação dos anfíbios. Como resultado, atualmente são conhecidas mais de 600 espécies de anfíbios que ocorrem na MA. Dentro deste bioma o Parque Nacional do Caparaó (PNC) é relevante, pois inclui o ponto mais alto da Mata Atlântica, o Pico da Bandeira com cerca de 3000 m de elevação, assim como diferentes fitofisionomias, como campos rupestres e florestas úmidas. Apesar disso, sua fauna de anfíbios é ainda pobremente descrita. Realizamos inventários de anfíbios no PNC e entorno de 2016 a 2018 e registramos 47 espécies de anuros, das quais duas são endêmicas e pelo menos seis ainda não foram descritas. Adicionalmente, compilamos dados de coletas anteriores (2004 a 2008) e dados secundários de coleções científicas. Ao juntar todos os dados registramos um total de 61 espécies de anuros de 12 famílias para o PNC e arredores, colocando esta área entre as 10 áreas mais ricas em anfíbios da MA. Algumas destas espécies estão representadas apenas por um ou dois exemplares em coleções e não foram registradas no PNC desde a década de 1980, como Thoropa lutzi e Hylodes vanzolinii. Estas espécies podem ser exemplos de declínios populacionais ou mesmo de extinções locais, destacando a necessidade de maiores esforços amostrais neste local altamente biodiverso.

Chemical characterization of the lipids in femoral gland secretions of wild male tegu lizards, Salvator merianae (Squamata, Teiidae) in comparison with captive-bred males

Although chemical interactions play an essential role in lizard social behavior, the chemical composition of the femoral gland secretions that many lizards use for communication is known for only a few species, mainly European Lacertids. The tegu lizard, Salvator merianae, is the only species of the Teiidae family for which there is available information on lipids in femoral secretions, but only for captive bred males from Argentina. Here, based on mass spectra obtained by GC-MS, we found 69 lipophilic compounds in femoral gland secretions of wild males S. merianae from Brazil, including cholesterol and high amounts of saturated fatty acids (mainly hexadecanoic and octadecanoic). We found contrasting differences between wild and captive-bred males, which lack cholesterol but present high amount of 9,12-octadecadienoic acid. These within-species differences between wild and captive lizards strongly suggest the important influence of different diets on the chemical composition of the femoral gland secretion and suggest caution when interpreting results from captive animals, even in the same species.

Rain forest shifts through time and riverine barriers shaped the diversification of South American terrestrial pit vipers (Bothrops jararacussu species group)

Aim To investigate (a) historical biogeographical connections and species interchange among rain forest habitats and (b) the role of riverine barriers on population divergence and speciation in the Neotropical region. Location Amazonia and Atlantic Forest in South America. Taxon Bothrops jararacussu species group (Serpentes: Viperidae). Methods We inferred phylogenetic relationships within Bothrops with an emphasis on the jararacussu species group under a Bayesian framework based on six molecular loci. We also used genetic coalescent simulations and approximate Bayesian computation to infer historical demography within the jararacussu group based on tests of alternative scenarios. Results We found the jararacussu species group to be monophyletic. The Atlantic Forest species B. pirajai and B. muriciensis were inferred nested within this group, closely related to B. jararacussu, confirming that Atlantic Forest species form a clade. The historical demographic analyses support vicariant separation between populations of B. brazili north and south of the Amazon River during the Miocene–Pliocene border, as well as colonization of the Atlantic Forest by a northern Amazonian ancestor in the Pleistocene. Main Conclusion The evolutionary history of the jararacussu species group sheds light on the dynamism of Neotropical rain forests over time, with at least one event of forest expansion leading to faunal interchange between Amazonian and Atlantic forests in the Pleistocene. Moreover, tests of alternative demographic scenarios suggest that the populations of B. brazili from north and south of the Amazon River originated from a vicariant event during the Miocene–Pliocene border, in agreement with the proposed age of establishment of the modern Amazon River drainage. Our results also have taxonomic implications for these medically important venomous snakes, supporting unrecognized diversity at the species level.

Not always young: The first vertebrate ancient origin of true parthenogenesis found in an Amazon leaf litter lizard with evidence of mitochondrial haplotypes surfing on the wave of a range expansion.

In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. In the Amazon region, parthenogenetic lizards of the Loxopholis percarinatum complex are widely distributed, comprising both diploid and triploid clones. Recently, putative males of L. percarinatum were reported, suggesting the existence of bisexual populations based on morphological data. Here, we used mitochondrial and nuclear data to investigate the origin of parthenogenesis in Loxopholis. Mitochondrial DNA analysis revealed three major lineages: unisexual/2n, unisexual/3n and bisexual, the last of which comprised two sub-lineages placed as the sister taxon to the unisexual/3n lineage. Genetic divergence among the lineages was ∼10% but was lower between the unisexual/3n and bisexual lineages (∼6%). Both mtDNA and nuDNA indicated that individuals from the bisexual lineages might belong to a new species. Nuclear DNA evidence indicates that crossings occasionally occur between unisexual 2n and males from the new bisexual species. Phylogenetic analysis of nuDNA showed L. ferreirai as the closest described bisexual species to the complex. Our results revealed an ancient origin of parthenogenesis in the L. percarinatum complex, in contrast to most young (Pleistocene) parthenogenetic lizards described thus far. Two hybridization events seem to have been involved: the first event occurred in late Miocene, between the ancestral lineage ("A") of the new bisexual species (as a maternal species) and the ancestral lineage of L. ferreirai, as a paternal species of L. percarinatum 2n; and the second event occurred in Pliocene-Pleistocene, in a backcross between L. percarinatum 2n and a male from the common ancestor ("B") of the new bisexual species giving rise to the lineage of L. percarinatum 3n. With these results, we showed that L. percarinatum complex also includes, at least, one undescribed bisexual species in addition to the two known parthenogenetic lineages (2n and 3n). Finally, we present evidence that diploid individuals of L. percarinatum experienced an event of wide demographic expansion over the past million years under an allele surfing model.

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna.

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post-Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability," highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.

Phenotypic and life-history diversification in Amazonian frogs despite past introgressions.

The advent of genomics in phylogenetics and population genetics strengthened the perception that conflicts among gene trees are frequent and often due to introgression. However, hybridization occurs mostly among species that exhibit little phenotypic differentiation. A recent study delineating species in Anomaloglossus, a frog genus endemic to the Guiana Shield, identified an intriguing pattern in the A. baeobatrachus species complex. This complex occurs in French Guiana and Amapá (Brazil) and comprises two sympatric phenotypes contrasting not only in body size, habitat, and advertisement call, but also in larval development mode (endotrophic vs exotrophic tadpoles). However, molecular and phenotypic divergences are, in some cases, incongruent, i.e specimens sharing mtDNA haplotypes are phenotypically distinct, suggesting a complex evolutionary history. Therefore, we genotyped 106 Anomaloglossus individuals using ddRADseq to test whether this phenotype/genotype incongruence was a product of phenotypic plasticity, incomplete lineage sorting, multiple speciation events, or admixture. Based on more than 16,000 SNPs, phylogenetic and population genetic approaches demonstrated that exotrophic populations are paraphyletic. Species tree and admixture analyses revealed a strikingly reticulate pattern, suggesting multiple historical introgression events. The evolutionary history of one exotrophic population in northern French Guiana is particularly compelling given that it received genetic material from exotrophic ancestors but shows very strong genetic affinity with the nearby endotrophic populations. This suggests strong selection on larval development and mating call after secondary contact and hybridization. The case of A. baeobatrachus represents a striking example of introgression among lineages that are phenotypically distinct, even in their larval development mode, and highlights how high-resolution genomic data can unravel unexpectedly complex evolutionary scenarios.