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Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.

Limbless lizards of the genus Anniella are found in the western United States and Mexico. Until recently only two species were known, but four new species have since been described. Since these lizards are fossorial, not much is known about the nature of gene flow within species, or if gene flow occurs across species boundaries in regions of overlap. Since these lizards are of conservation interest, we isolated and developed nine tetranucleotide microsatellite loci for the recently described species Anniella alexanderae. We characterized the polymorphism of each locus in A. alexanderae, and then cross-amplified these loci in five other Anniella species. These nine loci have high observed levels of heterozygosity and polymorphism information content, and were in Hardy-Weinberg equilibrium within the A. alexanderae samples we tested, indicating that they will have high utility in assessing population genetic and demographic patterns within Anniella.

The cloud forests of Mesoamerica are notable for their high endemism, and plethodontid salamanders provide a striking example of divergence and microendemism across cloud forest blocks at a regional level. Salamanders that make use of arboreal bromeliad microhabitats in the cloud forest appear to be especially prone to divergence driven by natural habitat fragmentation, and are expected to show high endemism at small spatial scales. We use a multilocus dataset to investigate the biogeographic history and relationships among species of a small genus of salamander, Cryptotriton, restricted to the cloud forests of Nuclear Central America. We use a morphological data set along with a coalescent species delimitation method to reveal the presence of at least one undescribed species from an isolated cloud forest in eastern Guatemala. Biogeographic analyses show that Cryptotriton has a different biogeographic history than another clade of cloud forest-restricted salamanders in the same region, perhaps indicating that each genus restricted the spatial expansion and diversification of the other through preemptive occupancy. Our results suggest that isolation across relatively short geographic distances has led to range fragmentation and deep divergence between species. Exploration of remaining patches of cloud forest likely will continue to reveal undetected diversity.

Phylogenetic relationships among species of the salamander family Salamandridae are investigated using nearly 3000 nucleotide bases of newly reported mitochondrial DNA sequence data from the mtDNA genic region spanning the genes tRNALeu-COI. This study uses nearly comprehensive species-level sampling to provide the first complete phylogeny for the Salamandridae. Deep phylogenetic relationships among the three most divergent lineages in the family Salamandrina terdigitata, a clade comprising the "True" salamanders, and a clade comprising all newts except S. terdigitata are difficult to resolve. However, most relationships within the latter two lineages are resolved with robust levels of branch support. The genera Euproctus and Triturus are statistically shown to be nonmonophyletic, instead each contains a diverse set of lineages positioned within the large newt clade. The genus Paramesotriton is also resolve as a nonmonophyletic group, with the newly described species P. laoensis constituting a divergent lineage placed in a sister position to clade containing all Pachytriton species and all remaining Paramesotriton species. Sequence divergences between P. laoensis and other Paramesotriton species are as great as those comparing P. laoensis and species of the genera Cynops and Pachytriton. Analyses of lineage diversification across the Salamandridae indicate that, despite its exceptional diversity, lineage accumulation appears to have been constant across time, indicating that it does not represent a true species radiation.

As part of an ongoing project to generate a mitochondrial database for terrestrial tortoises based on museum specimens, the complete mitochondrial genome sequences of 10 species and a ~;14 kb sequence from an eleventh species are reported. The sampling of the present study emphasizes Mediterranean tortoises (genus Testudo and their close relatives). Our new sequences are aligned, along with those of two testudinoid turtles from GenBank, Chrysemys picta and Mauremys reevesii, yielding an alignment of 14,858 positions, of which 3,238 are parsimony informative. We develop a phylogenetic taxonomy for Testudo and related species based on well-supported, diagnosable clades. Several well-supported nodes are recovered, including the monophyly of a restricted Testudo, T. kleinmanni + T. marginata (the Chersus clade), and the placement of the enigmatic African pancake tortoise (Malacochersus tornieri) within the predominantly Palearctic greater Testudo group (Testudona tax. nov.). Despite the large amount of sequence reported, there is low statistical support for some nodes within Testudona and so we do not propose names for those groups. A preliminary and conservative estimation of divergence times implies a late Miocene diversification for the testudonan clade (6-12 million years ago), matching their first appearance in the fossil record. The multi-continental distribution of testudonan turtles can be explained by the establishment of permanent connections between Europe, Africa, and Asia at this time. The arrival of testudonan turtles to Africa occurred after one or more initial tortoise invasions gave rise to the diverse (>25 species) 'Geochelone complex.' Two unusual genomic features are reported for the mtDNA of one tortoise, M. tornieri: (1) nad4 has a shift of reading frame that we suggest is resolved by translational frameshifting of the mRNA on the ribosome during protein synthesis and (2) there are two copies of the control region and trnF, with the latter having experienced multiple nucleotide substitutions in a pattern suggesting that each is being maintained by selection.

Evolutionary biologists are always interested in deciphering the geographic context of diversification, therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region. Here, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asianendemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222 samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding, mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern China. Those ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP). Particularly, the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those newts. However, despite differences in realized niches between lineages, there is no evidence for divergence of fundamental niches. Preservation of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of speciation. Based on those results, we advocate a multi-pronged protection strategy for newts in the three genera. [ABSTRACT FROM AUTHOR]

Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans , TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269 Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68 Mb and N90 = 19 Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution. [ABSTRACT FROM AUTHOR]