Dehydration alters behavioral thermoregulation and the geography of climatic vulnerability in two Amazonian lizards.

High temperatures and low water availability often strike organisms concomitantly. Observing how organisms behaviorally thermohydroregulate may help us to better understand their climatic vulnerability. This is especially important for tropical forest lizards, species that are purportedly under greater climatic risk. Here, we observed the influence of hydration level on the Voluntary Thermal Maximum (VTmax) in two small Amazonian lizard species: Loxopholis ferreirai (semiaquatic and scansorial) and Loxopholis percarinatum (leaf litter parthenogenetic dweller), accounting for several potential confounding factors (handling, body mass, starting temperature and heating rate). Next, we used two modeling approaches (simple mapping of thermal margins and NicheMapR) to compare the effects of dehydration, decrease in precipitation, ability to burrow, and tree cover availability, on geographic models of climatic vulnerability. We found that VTmax decreased with dehydration, starting temperature, and heating rates in both species. The two modeling approaches showed that dehydration may alter the expected intensity, extent, and duration of perceived thermal risk across the Amazon basin for these forest lizards. Based on our results and previous studies, we identify new evidence needed to better understand thermohydroregulation and to model the geography of climatic risk using the VTmax.

Draft genome and multi-tissue transcriptome assemblies of the Neotropical leaf-frog Phyllomedusa bahiana.

Amphibians are increasingly threatened worldwide, but the availability of genomic resources that could be crucial for implementing informed conservation practices lags well behind that for other vertebrate groups. Here, we describe draft de novo genome, mitogenome, and transcriptome assemblies for the Neotropical leaf-frog Phyllomedusa bahiana native to the Brazilian Atlantic Forest and Caatinga. We used a combination of PacBio long reads and Illumina sequencing to produce a 4.74-Gbp contig-level genome assembly, which has a contiguity comparable to other recent nonchromosome level assemblies. The assembled mitogenome comprises 16,239 bp and the gene content and arrangement are similar to other Neobratrachia. RNA-sequencing from 8 tissues resulted in a highly complete (86.3%) reference transcriptome. We further use whole-genome resequencing data from P. bahiana and from its sister species Phyllomedusa burmeisteri, to demonstrate how our assembly can be used as a backbone for population genomics studies within the P. burmeisteri species group. Our assemblies thus represent important additions to the catalog of genomic resources available from amphibians.

The first mitochondrial genome of a South America parthenogenetic lizard (Squamata: Gymnophthalmidae).

The mitogenome of the South American parthenogenetic lizard Loxopholis percarinatum Müller, 1923 (Squamata: Gymnophthalmidae), a uni-bisexual species complex, was recovered for three individuals from Rio Negro region, Amazonas, Brazil. The content and order of genes are typical for vertebrate mitochondrial genomes, and we recovered 13 protein-coding genes, 22 tRNA, and two rRNA (12S and 16S), in addition to partial fragments of the Control Region. A maximum likelihood phylogenetic analysis with mitogenomes of selected lizard families recovered L. percarinatum with Iphisa elegans Gray, 1851, the only other Gymnophthalmidae species available in GenBank.

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.

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.

Gene and species trees of a Neotropical group of treefrogs: genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species.

The Neotropical Phyllomedusa burmeisteri treefrog group includes four diploid (P. bahiana, P. burmeisteri, P. distincta and P. iheringii) and one tetraploid (P. tetraploidea) forms. Here we use mitochondrial and nuclear sequence variation from across its range to verify if recognized morphospecies correspond to phylogenetic clades, examine the origin of the polyploid P. tetraploidea, and compare range wide patterns of diversification to those of other BAF organisms. We compared single gene trees with one Bayesian multi-gene tree, and one Bayesian species tree inferred under a coalescent framework. Our mtDNA phylogenetic analyses showed that P. bahiana, P. burmeisteri and P. iheringii correspond to monophyletic clades, while P. distincta and P. tetraploidea were paraphyletic. The nuclear gene trees were concordant in revealing two moderately supported groups including (i) P. bahiana and P. burmeisteri (northern species) and (ii) P. distincta, P.tetraploidea and P. iheringii (southern species). The multi-gene tree and the species tree retrieved similar topologies, giving high support to the northern and southern clades, and to the sister-taxa relationship between P. tetraploidea and P. distincta. Estimates of (t)MRCA suggest a major split within the P. burmeisteri group at ≈ 5 Myr (between northern and southern groups), while the main clades were originated between ≈ 0.4 and 2.5 Myr, spanning the late Pliocene and Pleistocene. Patterns of geographic and temporal diversification within the group were congruent with those uncovered for other co-distributed organisms. Independent paleoecological and geological data suggest that vicariance associated with climatic oscillations and neotectonic activity may have driven lineage divergence within the P. burmeisteri group. P. tetraploidea probably originated from polyploidization of P. distincta or from a common ancestor.