Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Distinct latitudinal patterns of molecular rates across vertebrates

The latitudinal diversity gradient (LDG) is the most notable global biodiversity pattern, but its underlying mechanisms remain unresolved. The evolutionary speed hypothesis (ESH) posits that molecular rates play a crucial role in shaping the LDG, suggesting that higher temperatures accelerate molecular rates, thereby facilitating rapid speciation and accumulation of biodiversity in the tropics. However, whether ESH can explain the LDG across diverse taxonomic groups remains debated, and systematic examinations of its two key predictions using consistent datasets and methodologies across vertebrates are lacking. Here, we tested ESH using molecular rates from mitochondrial (5,424 species) and nuclear (1,512 species) genomes across major vertebrate groups, including fishes, amphibians, reptiles, mammals, and birds. Our findings revealed distinct latitudinal patterns in the absolute synonymous substitution rate (dS), which were influenced by thermoregulatory strategies. Specifically, the dS increases with ambient temperature and decreases with latitude in ectotherms but shows no correlation in most endotherms. These distinct patterns are likely attributed to different key predictors of dS between thermogroups, with temperature playing a major role only in ectotherms. For mitochondrial genes, absolute nonsynonymous substitution rates (dN) increase with temperature, likely driven by mutation rates in ectotherms and purifying selection in endotherms. However, neither mitochondrial dS nor dN correlates with diversification rates across vertebrates, contradicting the second prediction of ESH. For nuclear rates, the ESH was supported in reptiles and amphibians but not in mammals, birds, or fishes. In conclusion, our results provide limited support for ESH in vertebrates, underscoring the intricate processes that shape the LDG.

Genomic Insights into Fertilization: Tracing PLCZ1 Orthologs Across Amphibian Lineages

Fertilization triggers a cascade of events, including a rise in egg cytosolic calcium that marks the onset of embryonic development. In mammals and birds, this critical process is mediated by the sperm-derived phospholipase C zeta (PLCζ), which is pivotal in releasing calcium from the endoplasmic reticulum in the egg and initiating embryonic activation. Intriguingly, Xenopus laevis, a key model organism in reproductive biology, lacks an annotated PLCZ1 gene, prompting questions about its calcium release mechanism during fertilization. Using bioinformatics and RNA sequencing of adult X. laevis testes, we investigated the presence of a PLCZ1 ortholog in amphibians. While we identified PLCZ1 homologs in 25 amphibian species, including 14 previously uncharacterized orthologs, we found none in X. laevis or its close relative, Xenopus tropicalis. Additionally, we found no compensatory expression of other PLC isoforms in these species. Synteny analysis revealed a PLCZ1 deletion in species within the Pipidae family and another intriguing deletion of potential sperm factor PLCD4 in the mountain slow frog, Nanorana parkeri. Our findings indicate that the calcium release mechanism in frog eggs involves a signaling pathway distinct from the PLCζ-mediated process observed in mammals.

Enhanced dynamicity: evolutionary insights into amphibian mitogenomes architecture

Mitogenomes are known for their structural dynamics and the complexity of their rearrangement patterns. However, their utility in metazoan comparative biology has not been fully exploited. Vertebrate mitogenomes are now sufficiently representative to allow the development of more advanced methods for comparing genome architecture. Furthermore, the relatively robust phylogeny of vertebrates at higher taxonomic ranks allows us to infer the patterns of genome evolution accordingly. In this study, using amphibians as an example, we performed data cleaning and manual annotation on 1777 samples from the NCBI and identified 88 rearrangement types, most of which were clade-specific. In addition, we quantified genomic changes in an evolutionary framework and obtained stepwise growth curves of the architectural changes. This study provides new perspectives for understanding the evolution of the mitogenomes in amphibians and is expected to facilitate the qualitative and quantitative development of mitogenomes research.

Re-examination of the oldest known frog from South America: New data prompt new evolutionary interpretations

Available paleontological evidence, although scarce, points to the early diversification of salientian lissamphibians in the Triassic and Early Jurassic. This study provides new key anatomical information on the earliest mostly articulated frog currently known, thereby improving our understanding of the early evolution of this lissamphibian lineage. Herein, available specimens of the Early Jurassic Vieraella herbstii from Patagonia, which consist of dorsal and ventral imprints of the incomplete, partially articulated skeleton of a single individual, are thoroughly redescribed. Although we comment on its known features, we focus on those that had been misinterpreted or overlooked previously. Among other features, we address the relative proportions of the skull regions and limbs, the morphology of the vomers, the peculiar articulation of the palatine flanges of premaxilla and maxilla that suggests the presence of well-developed cristae subnasales, and the presence of prepollex. The most surprising, significant findings are the presence of stapes, indicating the possibility of a complete tympanic middle ear, and of a short, tapering urostyle and postsacral vertebral elements. Based on available information, we present partial reconstructions of the pectoral girdle and the skeleton of Vieraella in the dorsal aspect. Discussion of the evolutionary significance of these features and perusal of the phylogenetic and functional analyses that included Vieraella in the taxon sampling highlight the necessity of thorough revision of the scorings and measurements, incorporating information presented herein. This reassessment will be relevant not only to clarify its relationships but also to provide sound insights into the early diversification of frogs.

Three new species of torrent treefrogs (Anura, Hylidae) of the Hyloscirtusbogotensis group from the eastern Andean slopes and the biogeographic history of the genus

The Hyloscirtusbogotensis group contains 17 species of treefrogs from the tropical Andes and Central America. A taxonomic review of the Amazonian clades of this group is presented based on DNA sequences of nuclear and mitochondrial DNA and a preliminary phylogenomic analysis of ultraconserved elements, as well as morphological, bioacoustic, and environmental characters. Additionally, the role of the Andes in the diversification of the genus Hyloscirtus is explored by reconstructing their ancestral basin (Amazon, Pacific, Caribbean). Our integrative analysis indicates the existence of eight undescribed candidate species within the group. Three of those species are described, previously masked within H.albopunctulatus, H.phyllognathus, and H.torrenticola. A lectotype is also designated for Hylaalbopunctulata. The new evidence suggests that neither Hyloscirtusphyllognathus nor H.torrenticola occur in Ecuador. The new species, H.elbakyanae sp. nov., H.dispersus sp. nov., and Hyloscirtusmaycu sp. nov. differ from other members of the group in bioacoustics and external morphology. The most useful diagnostic characters among species were advertisement calls. In contrast, skin coloration is highly variable intraspecifically and, as a result, of low diagnostic value. High variation in color is partly a result of phenotypic plasticity. Our biogeographic reconstructions indicate that the Andean barrier influenced the diversification of Hyloscirtus. Since the early Oligocene, there have been only four colonization events across de Andes, between the Pacific and Amazon basins. Two of those events occurred more than 14 Mya, when most of the tropical Andes were below 3000 m. Species in the highland H.larinopygion group are younger, suggesting recent diversification as high montane forests and paramo habitats emerged.

A time-calibrated salamander phylogeny including 765 species and 503 genes

Recent time-calibrated amphibian phylogenies agree on the family-level relationships among extant salamanders but had disparate sampling regimes and inferred very different divergence times. For example, a recent phylogenomic study based on 220 nuclear loci had limited taxon sampling (41 species) and estimated relatively young divergence dates, whereas a more extensive supermatrix study based on 15 genes and 481 species estimated dates that were 22-45 million years older for major clades. Here, we combined phylogenomic and supermatrix approaches to estimate the largest salamander phylogeny to date based on molecular markers. Our matrix contained 765 salamander species and 503 genes (with 92.3% missing data overall). We included 284 more species than the previous largest salamander phylogeny (59% increase) and sampled approximately 93% of all currently described salamander species. Our dating analyses incorporated more than twice as many fossil calibration points within salamanders as previous studies. Maximum-likelihood estimates of tree topology yielded family-level relationships that were consistent with earlier studies. Nearly all species were placed in the expected genera, despite extensive missing data in many species. Bootstrap support was generally high across the tree but was poor in some clades where sampling of genes was limited (e.g., among some bolitoglossine salamanders). The dating analyses yielded age estimates for major clades that were generally intermediate between those from the previous phylogenomic and supermatrix analyses. We also provide a set of 200 time-calibrated trees for use in comparative analyses.

Phylogenetics, biogeography, and life history evolution in the broadly distributed treefrog genus Dendropsophus (Anura: Hylidae: Hylinae)

Dendropsophusis one of the most species-rich genera of hylid treefrogs. Recent studies integrating Sanger-generated mitochondrial and nuclear loci with phenomic characters (SP) have advanced understanding of this clade, but questions about its internal relationships and biogeographic history persist. To address these questions, we used anchored hybrid enrichment (AHE) to combine 432 nuclear loci for 78 taxa (72 % of species) with published data. Quantitatively, the impact of the AHE data was modest, with compositional differences in only three recognized clades and more than 80 % of the clades in the AHE + SP analyses also supported in the SP-only analyses. Nevertheless, the impact of AHE was crucial for resolving and increasing support for multiple nodes. We transferred one species of the formerD. ruschiigroup to theD. decipiensgroup and redefined theD. leucophyllatusgroup to avoid paraphyly. We estimated divergence times to reconstruct the clade's biogeographic history. We also examined evolution of oviposition sites and assessed its effect on lineage accumulation. Dendropsophuslikely originated ∼ 57 mya, predating the Andean uplift, with some taxa showing dispersal patterns less constrained by ecological changes than previously thought.

Phylogenomics yields new systematic and taxonomical insights for Lissotriton newts, a genus with a strong legacy of introgressive hybridization

The ease with which genome-wide data can nowadays be collected allows complicated phylogenetic questions to be re-evaluated. Phylogenetic relationships among newts have often proven difficult to resolve due to the prevalence of incomplete lineage sorting and introgressive hybridization. For the newt genus Lissotriton, phylogenetic relationships are not settled and there is controversy surrounding the species status of several taxa. We obtain c. 7 k nuclear DNA markers with target enrichment by sequence capture and conduct a concatenated analysis with RAxML, gene-tree summarization with ASTRAL, and species tree estimation with SNAPPER. We explore introgression between evolutionary lineages with TreeMix and Dsuite and compare how introgression events influence the different phylogenetic tools employed. We retrieve tree topologies that are discordant with previous mtDNA-based attempts, particularly concerning the phylogenetic placement of L. italicus and the L. vulgaris species complex. Yet, we also observe deviations between the phylogenetic hypotheses resulting from the different analyses. We interpret the placement of L. montandoni deep within the L. vulgaris species complex by SNAPPER, rather than as the sister taxon to the remainder of the L. vulgaris species complex according to RAxML and ASTRAL, as an artifact of introgression - well-documented in previous work and backed up by TreeMix and Dsuite analyses. Our analyses allow us to make some taxonomical recommendations: we confirm the recently proposed species status of L. kosswigi and L. graecus and propose that L. v. lantzi and L. v. schmidtleri had better be treated as subspecies. Our work also highlights areas for further taxonomic research: range-wide phylogenomic data are required to disentangle the L. boscai - L. maltzani species complex and the northern and southern lineages of L. v. vulgaris. Our study illustrates the power of target enrichment by sequence capture in tackling longstanding questions in taxa with an extensive history of hybridization and introgression.

Primary regulatory T cell activator FOXP3 is present across Amphibia

The overall structure of the immune system is highly conserved across jawed vertebrates, but characterization and description of the immune system is heavily biased toward mammals. One arm of the vertebrate immune system, the adaptive immune system, mounts pathogen-specific responses that tend to be robust and effective at clearing pathogens. This system requires selection against self-recognition and modulation of the immune response. One of the mechanisms of immune modulation is the presence of regulatory T cells that suppress other effector immune cells. Regulatory T cells and their primary activator forkhead box protein P3 (FOXP3) have been well characterized in mammalian models but unexplored in most other vertebrate taxa. Amphibians are a good focal group for the characterization of FOXP3 due to their phylogenetic position on the vertebrate tree of life, and their susceptibility to emerging pathogens. In this study, we mined available transcriptomic and genomic data to confirm the presence of FOXP3 across the amphibian tree of life. We find that FOXP3 is present in all major clades of amphibians. We also test whether selection on FOXP3 shows signatures of intensification among the three main clades of amphibians, which may reflect shifts in the stringency of natural selection on this gene. Our findings provide insights into the evolutionary history of the vertebrate immune system and confirm the conservation of vertebrate immune genes within amphibians.

The Limits of the Metapopulation: Lineage Fragmentation in a Widespread Terrestrial Salamander (Plethodon cinereus)

In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here, we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least 6 divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in Bayesian Phylogenetics and Phylogeography supported 5 lineages of P. cinereus, genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence.

Complex Models of Sequence Evolution Improve Fit, But Not Gene Tree Discordance, for Tetrapod Mitogenomes

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial data sets as the previous study using 2 additional, more complex models of sequence evolution that each include a different biologically realistic aspect of the evolutionary process: A covarion model to incorporate site-specific rate variation across lineages (heterotachy), and a partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could, in fact, be biological in nature after all.

A Genetic Polymorphism Underlying Alternative Reproductive Tactics in Eurycea Salamanders

Alternative reproductive tactics are discrete, intrasexual differences in reproductive behaviour within a population. In some cases, these complex phenotypes are determined by autosomal supergenes or sex chromosomes-both of which exhibit reduced recombination and thus enable the linked inheritance of co-adapted alleles from multiple loci. Most alternative reproductive tactics in amphibians are plastic (and reversible), environmentally determined and lacking morphological differentiation, but a striking exception is found in the two-lined salamander (Eurycea bislineata) species complex. In some populations, two distinct male phenotypes coexist: 'searching' males have mental glands, protruding premaxillary teeth and elongate cirri used in terrestrial courtship, while 'guarding' males lack these traits and instead have hypertrophied jaw musculature used in mate guarding at aquatic nesting sites. These tactics differ in many morphological and behavioural phenotypes, but their proximate cause has not yet been described. Here, we generated genome-wide SNP data from > 130 Eurycea cf. wilderae collected from Highlands Biological Station. We provide evidence for an XY sex determination and for a Y-linked polymorphism underlying alternative reproductive tactics in this population. We then develop and validate a PCR-based genotyping assay and apply it to characterise the sex ratio and relative frequency of male tactics from a sample of larvae. Our results add to the growing body of literature exploring the importance of supergenes and sex chromosomes in complex intraspecific polymorphisms, and we highlight opportunities for future work to continue exploring the genomic architecture of these traits.

Developmental sequence of the chondrocranium in the obligate carnivorous larvae of Lepidobatrachus laevis (Amphibia: Ceratophryidae)

The vertebrate head and its skull represent a significant innovation that has played a key role in the evolutionary and ecological success of vertebrates. For a global and integral understanding of the evolution of the head skeleton, it is essential to have reliable information on the development of chondrocranium in a wide range of vertebrate species. Therefore, we studied the cranial chondrogenesis of the larva of the Budgett frog, Lepidobatrachus laevis (Ceratophryidae, Neobatrachia). We studied the development using several methods, including histological preparation of transverse sections of the chondrocranium, morphological analysis of three different states of development (mesenchymal aggregation, differentiation, and chondrification), and three-dimensional digital reconstructions. As a result, we observed that the Anlage of the chondrocranium at Gosner stage 19 is laterally compressed, that is, it is initially higher than wide. It gradually flattens, enlarges, and differentiates until reaching a very wide and flat shape at Gosner stage 26. Furthermore, we show that the chondrocranial development of L. laevis takes place in a mosaic pattern, which differs to nontetrapod vertebrates in which an anterior to posterior gradient of chondrification is observed. We identified 19 developmental stages in L. laevis according to the chondrification state of its cranial structures. The first element reaching the differentiation-into-chondroblast stage is the hypobranchial plate of the branchial basket, and chondrification, that is, final differentiation, occurs simultaneously in several structures of the neurocranium and viscerocranium. We hypothesize that the rapid chondrification of L. laevis' chondrocranium is an adaptation to the semi-arid climate conditions from its type locality, El Gran Chaco in South America. Due to the only temporary availability of suitable water accumulations this apparent accelerated development would make sense to ensure the tadpoles are froglets by the time the water body disappears. Here, we provide novel information on chondrocranial development in L. laevis. We compare our results to the developmental sequences, previously known from other vertebrate taxa, particularly within the amphibian phylogeny, in an attempt to understand developmental variability and the evolutionary history of the vertebrate head skeleton.

A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography

The genus Sylvirana includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for Sylvirana and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and COI) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus Sylvirana to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling. Our results conservatively reveal six undescribed species, mostly distributed in peninsular Indochina. Phylogenetic analyses strongly support the non-monophyly of Sylvirana with respect to Pterorana. Additionally, phylogenetic results place Sylvirana guentheri and Pelophylax lateralis into genus Humerana, supporting the inclusion of Hylarana latouchii, Papurana milleti, and Hylarana attigua within Pterorana + Sylvirana. The long-disputed species of Hylarana bannanica (previously Sylvirana) cluster with genus Papurana. Because the results of multiple non-monophyletic genera create taxonomic confusion, we suggest relegating all genera to subgenus rank of Hylarana. Sylvirana is a junior synonym of the Pterorana. Biogeographically, we trace the origin of Pterorana to Southeast Asia during the early Miocene, with subsequent dispersal thereafter. Our study shows that climatic changes may have profoundly influenced the diversification of Pterorana during the Miocene.

Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.

The small and inconspicuous majority: Revealing the megadiversity and historical biogeography of the Pristimantis unistrigatus species group (Anura, Strabomantidae)

With more than 600 recognized species, the genus Pristimantis is already the most diverse among vertebrates, but described species only represent a fraction of the actual diversity in this clade. This genus is widely distributed throughout the Neotropics and represents an interesting model for biogeographic studies because Pristimantis spp. are direct developing and generally have narrow ecological niches and low dispersal abilities. The P. unistrigatus species group is one of the most important components in the genus (ca. 200 recognized species) and has been supported by morphological but not by molecular evidence. We assessed the species boundaries and distribution in the P. unistrigatus species group and infer spatiotemporal patterns of diversification related to historical landscape changes in the Neotropics. We gathered three mitochondrial, and two nuclear DNA loci from 416 specimens throughout the range of the group, and including 68 nominal species. We redefine the group based on the obtained phylogeny and found 151 candidate species that composes it, with 83 of these remaining undescribed. We recovered 11 major clades within the group that diverged before 13 Ma. The diversification of the group started during the early Miocene most likely in northwestern South America, currently corresponding to western Amazonia and northern Andes. The other neotropical areas subsequently acted as sinks, receiving lineages mostly during the last 10 Ma, after the demise of the Pebas System and the setup of the modern Amazonian hydrographic system.

The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?

The orographic evolution of the Himalaya-Tibet Mountain system continues to be a subject of controversy, leading to considerable uncertainty regarding the environment and surface elevation of the Tibetan Plateau during the Cenozoic era. As many geoscientific (but not paleontological) studies suggest, elevations close to modern heights exist in vast areas of Tibet since at least the late Paleogene, implicating the presence of large-scale alpine environments for more than 30 million years. To explore a recently proposed alternative model that assumes a warm temperate environment across paleo-Tibet, we carried out a phylogeographic survey using genomic analyses of samples covering the range of endemic lazy toads (Scutiger) across the Himalaya-Tibet orogen. We identified two main clades, with several, geographically distinct subclades. The long temporal gap between the stem and crown age of Scutiger may suggest high extinction rates. Diversification within the crown group, depending on the calibration, occurred either from the Mid-Miocene or Late-Miocene and continued until the Holocene. The present-day Himalayan Scutiger fauna could have evolved from lineages that existed on the southern edges of the paleo-Tibetan area (the Transhimalaya = Gangdese Shan), while extant species living on the eastern edge of the Plateau originated probably from the eastern edges of northern parts of the ancestral Tibetan area (Hoh Xil, Tanggula Shan). Based on the Mid-Miocene divergence time estimation and ancestral area reconstruction, we propose that uplift-associated aridification of a warm temperate Miocene-Tibet, coupled with high extirpation rates of ancestral populations, and species range shifts along drainage systems and epigenetic transverse valleys of the rising mountains, is a plausible scenario explaining the phylogenetic structure of Scutiger. This hypothesis aligns with the fossil record but conflicts with geoscientific concepts of high elevated Tibetan Plateau since the late Paleogene. Considering a Late-Miocene/Pliocene divergence time, an alternative scenario of dispersal from SE Asia into the East, Central, and West Himalaya cannot be excluded, although essential evolutionary and biogeographic aspects remain unresolved within this model.

The Remarkable Diversity of Vertebrate Bitter Taste Receptors: Recent Advances in Genomic and Functional Studies

Bitter taste perception is crucial for animal survival. By detecting potentially harmful substances, such as plant secondary metabolites, as bitter, animals can avoid ingesting toxic compounds. In vertebrates, this function is mediated by taste receptors type 2 (T2Rs), a family of G protein-coupled receptors (GPCRs) expressed on taste buds. Given their vital roles, T2Rs have undergone significant selective pressures throughout vertebrate evolution, leading to frequent gene duplications and deletions, functional changes, and intrapopulation differentiation across various lineages. Recent advancements in genomic and functional research have uncovered the repertoires and functions of bitter taste receptors in a wide range of vertebrate species, shedding light on their evolution in relation to dietary habits and other ecological factors. This review summarizes recent research on bitter taste receptors and explores the mechanisms driving the diversity of these receptors from the perspective of vertebrate ecology and evolution.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

A time-calibrated phylogeny of the diversification of Holoadeninae frogs

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification. Aiming to fill this gap, we inferred the phylogenetic relationships and divergence times for Holoadeninae using molecular data and calibration information derived from the fossil record of Neobatrachia. Our inferred phylogeny confirmed most genus-level associations, and molecular dating analysis placed the origin of Holoadeninae in the Eocene, with subsequent splits also occurring during this period. The climatic and geological events that occurred during the Oligocene-Miocene transition were crucial to the dynamic biogeographical history of the subfamily. However, the wide highest posterior density intervals in our divergence time estimates are primarily attributed to the absence of Holoadeninae fossil information and, secondarily, to the limited number of sampled nucleotide sites.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution

Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.

Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification

The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].

Shape Evolution in Two Acts: Morphological Diversity of Larval and Adult Neoaustraranan Frogs

Phenotypic traits can evolve independently at different stages of ontogeny, optimizing adaptation to distinct ecological contexts and increasing morphological diversity in species with complex life cycles. Given the relative independence resulting from the profound changes induced by metamorphosis, niche occupation and resource utilization in tadpoles may prompt evolutionary responses that do not necessarily affect the adults. Consequently, diversity patterns observed in the larval shape may not necessarily correspond to those found in the adult shape for the same species, a premise that can be tested through the Adaptive Decoupling Hypothesis (ADH). Herein, we investigate the ADH for larval and adult shape differentiation in Neoaustrarana frogs. Neoaustrarana frogs, particularly within the Cycloramphidae family, exhibit remarkable diversity in tadpole morphology, making them an ideal model for studying adaptive decoupling. By analyzing 83 representative species across four families (Alsodidae, Batrachylidae, Cycloramphidae, and Hylodidae), we generate a morphological dataset for both larval and adult forms. We found a low correlation between larval and adult shapes, species with a highly distinct larval shape having relatively similar shape when adults. Larval morphological disparity is not a good predictor for adult morphological disparity within the group, with distinct patterns observed among families. Differences between families are notable in other aspects as well, such as the role of allometric components influencing shape and morphospace occupancy. The larval shape has higher phylogenetic structure than the adult. Evolutionary convergence emerges as a mechanism of diversification for both larval and adult shapes in the early evolution of neoaustraranans, with shape disparity of tadpoles reaching stable levels since the Oligocene. The widest occupation in morphospace involves families associated with dynamically changing environments over geological time. Our findings support the ADH driving phenotypic diversity in Neoaustrarana, underscoring the importance of considering ontogenetic stages in evolutionary studies.

Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae)

The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a "south-north" or a "north-south" direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines' ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.

Diversifying in the mountains: spatiotemporal diversification of frogs in the Western Ghats biodiversity hotspot

Mountain ranges are hotspots of biodiversity. However, the mechanisms that generate biodiversity patterns in different mountainous regions and taxa are not apparent. The Western Ghats (WG) escarpment in India is a globally recognized biodiversity hotspot with high species richness and endemism. Most studies have either invoked paleoclimatic conditions or climatic stability in the southern WG refugium to explain this high diversity and endemism. However, the factors driving macroevolutionary change remain unexplored for most taxa. Here, we generated the most comprehensive dated phylogeny to date for ranoid frogs in the WG and tested the role of paleoclimatic events or climatic stability in influencing frog diversification. We found that the diversity of different ranoid frog clades in the WG either accumulated at a constant rate through time or underwent a decrease in speciation rates around 3-2.5 Ma during the Pleistocene glaciation cycles. We also find no significant difference in diversification rate estimates across elevational gradients and the three broad biogeographic zones in the WG (northern, central, and southern WG). However, time-for-speciation explained regional species richness within clades, wherein older lineages have more extant species diversity. Overall, we find that global paleoclimatic events have had little impact on WG frog diversification throughout most of its early history until the Quaternary and that the WG may have been climatically stable allowing lineages to accumulate and persist over evolutionary time.

Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy

Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.

A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.

Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic

The iconic mountains of the Pantepui biogeographical region host many early-diverging endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient "Lost World". While this is the case of several frog lineages, others appear to have more recent origins, adding to the controversy around the diversification processes in this region. Due to its remoteness, Pantepui is challenging for biological surveys, and only a glimpse of its biodiversity has been described, which hampers comprehensive evolutionary studies in many groups. During a recent expedition to the Neblina massif on the Brazil-Venezuela border, we sampled two new frog species that could not be assigned to any known genus. Here, we perform phylogenetic analyses of mitogenomic and nuclear loci to infer the evolutionary relationships of the new taxa and support their description. We find that both species represent single lineages deeply nested within Brachycephaloidea, a major Neotropical clade of direct-developing frogs. Both species diverged >45 Ma from their closest relatives: the first is sister to all other Brachycephaloidea except for Ceuthomantis, another Pantepui endemic, and the second is sister to Brachycephalidae, endemic to the Brazilian Atlantic Forest. In addition to these considerable phylogenetic and biogeographic divergences, external morphology and osteological features support the proposition of two new family and genus-level taxa to accommodate these new branches of the amphibian tree of life. These findings add to other recently described ancient vertebrate lineages from the Neblina massif, providing a bewildering reminder that our perception of the Pantepui's biodiversity remains vastly incomplete. It also provides insights into how these mountains acted as "museums" during the diversification of Brachycephaloidea and of Neotropical biotas more broadly, in line with the influential "Plateau theory". Finally, these discoveries point at the yet unknown branches of the tree of life that may go extinct, due to global climate change and zoonotic diseases, before we even learn about their existence, amphibians living at higher elevations being particularly at risk.

Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements

Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.

A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.

The interglenoid tubercle of the atlas is ancestral to lissamphibians

Lissamphibians, represented today by frogs, salamanders, and caecilians, diverged deep in the tetrapod tree of life. Extensive morphological adaptations to disparate lifestyles have made linking extant lissamphibians to one another and to their extinct relatives difficult and controversial. However, the discovery of a feature on the atlas of the frog Xenopus laevis, may add to the small set of osteological traits that unite lissamphibians. In this study, we combine our observations of atlas development in X. laevis with a deep examination of atlantal interglenoid tubercle (TI) occurrence in fossil taxa. The TI is shown herein to occur transiently on the ossifying atlas of roughly one-third of X. laevis tadpoles but is absent in adults of this species. In ancestral character state estimations (ACSE), within the evolutionary context of lissamphibians as dissorophoid temnospondyls, this feature is found to be ancestrally shared among lissamphibians, its presence is uncertain in stem batrachians, and then the TI is lost in extant caecilians and frogs. However, our data suggests apparent TI loss around the origin of frogs may be explained by its ontogenetically transient nature. The only nonamphibian tetrapods with a TI are "microsaurs," and this similarity is interpreted as one of many convergences that resulted from convergent evolutionary processes that occurred in the evolution of "microsaurs" and lissamphibians. The TI is thus interpreted to be ancestral to lissamphibians as it is found to be present in some form throughout each extant lissamphibian clade's history.

Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity

The extant amphibians have developed uncanny abilities to adapt to their environment. I compared the genes of amphibians to those of other vertebrates to investigate the genetic changes underlying their unique traits, especially salamanders' regeneration and longevity. Using the well-supported Batrachia tree, I found that salamander genomes have undergone accelerated adaptive evolution, especially for development-related genes. The group-based comparison showed that several genes are under positive selection, rapid evolution, and unexpected parallel evolution with traits shared by distantly related species, such as the tail-regenerative lizard and the longer-lived naked mole rat. The genes, such as EEF1E1, PAFAH1B1, and OGFR, may be involved in salamander regeneration, as they are involved in the apoptotic process, blastema formation, and cell proliferation, respectively. The genes PCNA and SIRT1 may be involved in extending lifespan, as they are involved in DNA repair and histone modification, respectively. Some genes, such as PCNA and OGFR, have dual roles in regeneration and aging, which suggests that these two processes are interconnected. My experiment validated the time course differential expression pattern of SERPINI1 and OGFR, two genes that have evolved in parallel in salamanders and lizards during the regeneration process of salamander limbs. In addition, I found several candidate genes responsible for frogs' frequent vocalization and caecilians' degenerative vision. This study provides much-needed insights into the processes of regeneration and aging, and the discovery of the critical genes paves the way for further functional analysis, which could open up new avenues for exploiting the genetic potential of humans and improving human well-being.

The radiation continuum and the evolution of frog diversity

Most of life's vast diversity of species and phenotypes is often attributed to adaptive radiation. Yet its contribution to species and phenotypic diversity of a major group has not been examined. Two key questions remain unresolved. First, what proportion of clades show macroevolutionary dynamics similar to adaptive radiations? Second, what proportion of overall species richness and phenotypic diversity do these adaptive-radiation-like clades contain? We address these questions with phylogenetic and morphological data for 1226 frog species across 43 families (which represent >99% of all species). Less than half of frog families resembled adaptive radiations (with rapid diversification and morphological evolution). Yet, these adaptive-radiation-like clades encompassed ~75% of both morphological and species diversity, despite rapid rates in other clades (e.g., non-adaptive radiations). Overall, we support the importance of adaptive-radiation-like evolution for explaining diversity patterns and provide a framework for characterizing macroevolutionary dynamics and diversity patterns in other groups.

Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.

A conservation planning strategy applied to the evolutionary history of the mantellid frogs of Madagascar

Phylogenetic diversity is an increasingly applied metric used to maximize the representation of evolutionary history in spatial conservation planning. When following this approach, researchers commonly overlook sites with a relatively higher proportion of recently diverged endemic species, also known as centers of neo-endemism. Here we aim to demonstrate how targeting the conservation of different facets of diversity (taxonomic diversity, phylogenetic diversity and centers of endemism) can provide more cost-effective solutions to the conservation of the all evolutionary spectrum of biodiversity. We do so by using the mantellid frogs of Madagascar as a case study. Our results confirm that areas with high concentrations of neo-endemism can be effectively identified as conservation planning priorities only if we specifically target them. Neglecting areas that are poor in phylogenetic diversity may therefore compromise the maintenance of diversification processes, particularly when lesser proportions of the landscape are protected. This approach can be of particular interest to island ecosystems, since they often harbor unique and restricted evolutionary radiations.

Selection on Visual Opsin Genes in Diurnal Neotropical Frogs and Loss of the SWS2 Opsin in Poison Frogs

Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here, we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their behavior. Our analyses show that assessments of opsin diversification in across taxa could expand our understanding of the role of sensory system evolution in ecological adaptation.

Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity

Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the 'higher Curculionidae' remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.

Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)

In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae)

Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest

Background

The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex.

Methods

We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations.

Results

Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.

In Vitro Investigation of the Antibacterial Activity of Salamander Skin Peptides

Given the current and future costs of antibiotic-resistant bacteria to human health and economic productivity, there is an urgent need to develop new antimicrobial compounds. Antimicrobial peptides are a promising alternative to conventional antibiotics and other antimicrobials. Amphibian skin is a rich source of bioactive compounds, but the antibacterial properties of salamander skin peptides have been neglected. Here, we examined the in vitro ability of skin peptides from 9 species of salamander representing 6 salamander families to inhibit the growth of ESKAPE pathogens, which are bacteria that have developed resistance to conventional antibiotics. We also examined whether the skin peptides caused lysis of human red blood cells. Skin peptides from Amphiuma tridactylum had the greatest antimicrobial properties, completely inhibiting the growth of all bacterial strains except for Enterococcus faecium. Likewise, skin peptides from Cryptobranchus alleganiensis completely inhibited the growth of several of the bacterial strains. In contrast, skin peptide mixtures from Ambystoma maculatum, Desmognathus fuscus, Eurycea bislineata, E. longicauda, Necturus beyeri, N. maculosus, and Siren intermedia did not completely inhibit bacterial growth even at the highest concentrations. Finally, none of the skin peptide mixtures caused lysis of human red blood cells. Together, we demonstrate that salamander skin produces peptides with potent antibacterial properties. It remains to elucidate the peptide sequences and their antibacterial mechanisms.

Three new species of the Synapturanus rabus complex (Microhylidae: Otophryninae) in Colombia with a review of the genus Synapturanus

The Neotropical microhylid genus Synapturanus was represented by only three species for almost five decades and remains poorly known. Recently two new species were described from the Eastern Guyana Shield, one from Peru, and one from Brazil. We describe three new species related to the S. rabus species complex with known distribution only in western Amazonia, Colombia. The S. rabus complex consists of the smallest species in the genus; one of the new species is slightly larger than S. rabus and we describe its full osteology; the other two new species are smaller than S. rabus. We also described the call and larvae of one of the new species. We provide an updated diagnosis and review the available molecular and phenotypic data for the genus.  

Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach

Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.

The evolution of reproductive modes and life cycles in amphibians

Amphibians have undergone important evolutionary transitions in reproductive modes and life-cycles. We compare large-scale macroevolutionary patterns in these transitions across the three major amphibian clades: frogs, salamanders, and caecilians. We analyse matching reproductive and phylogenetic data for 4025 species. We find that having aquatic larvae is ancestral for all three groups and is retained by many extant species (33-44%). The most frequent transitions in each group are to relatively uncommon states: live-bearing in caecilians, paedomorphosis in salamanders, and semi-terrestriality in frogs. All three groups show transitions to more terrestrial reproductive modes, but only in caecilians have these evolved sequentially from most-to-least aquatic. Diversification rates are largely independent of reproductive modes. However, in salamanders direct development accelerates diversification whereas paedomorphosis decreases it. Overall, we find a widespread retention of ancestral modes, decoupling of trait transition rates from patterns of species richness, and the general independence of reproductive modes and diversification.

Historical biogeography highlights the role of Miocene landscape changes on the diversification of a clade of Amazonian tree frogs

The diversification processes underlying why Amazonia hosts the most species-rich vertebrate fauna on earth remain poorly understood. We studied the spatio-temporal diversification of a tree frog clade distributed throughout Amazonia (Anura: Hylidae: Osteocephalus, Tepuihyla, and Dryaderces) and tested the hypothesis that Miocene mega wetlands located in western and central Amazonia impacted connectivity among major biogeographic areas during extensive periods. We assessed the group’s diversity through DNA-based (16S rRNA) species delimitation to identify Operational Taxonomic Units (OTUs) from 557 individuals. We then selected one terminal for each OTU (n = 50) and assembled a mitogenomic matrix (~14,100 bp; complete for 17 terminals) to reconstruct a Bayesian, time-calibrated phylogeny encompassing nearly all described species. Ancestral area reconstruction indicates that each genus was restricted to one of the major Amazonian biogeographic areas (western Amazonia, Guiana Shield and Brazilian Shield, respectively) between ~10 and 20 Mya, suggesting that they diverged and diversified in isolation during this period around the Pebas mega wetland. After 10 Mya and the transition to the modern configuration of the Amazon River watershed, most speciation within each genus continued to occur within each area. In Osteocephalus, only three species expanded widely across Amazonia (< 6 Mya), and all were pond-breeders. Species with other breeding modes remained mostly restricted to narrow ranges. The spectacular radiation of Osteocephalus was probably driven by climatic stability, habitat diversity and the acquisition of new reproductive modes along the Andean foothills and western Amazonia. Our findings add evidence to the importance of major hydrological changes during the Miocene on biotic diversification in Amazonia.