Sean Michael Rovito

Asexual lineages are thought to experience elevated extinction rates compared with sexual species, yet direct evidence for the underlying genetic causes remains scarce. Muller's ratchet predicts that the absence of recombination in asexual organisms facilitates the accumulation of deleterious mutations, thereby reducing long-term fitness. Here, we test this hypothesis in the hybrid-origin, parthenogenetic whiptail lizard Aspidoscelis tesselatus by integrating short-read RNAseq and long-read IsoSeq data from both the asexual lineage and its parental sexual species. We reconstructed phased transcripts for A. tesselatus to quantify mutation accumulation relative to the parental sexual species. Comparative analyses revealed elevated ω ratios in both parental genomic complements (subgenomes) of the parthenogenetic lineage, consistent with accelerated accumulation of nonsynonymous mutations. Structural variant analyses identified multiple indels in expressed transcripts predicted to disrupt protein domains. Functional annotation indicated that genes affected by both single-nucleotide variants and indels were enriched for roles in chromatin organization, apoptosis regulation, and transcriptional control. While both parental subgenomes showed similar evolutionary patterns, the maternal complement exhibited more structural and missense mutations than the paternal complement. Together, these results provide evidence that mutations accumulate in asexual A. tesselatus in genes involved in core cellular functions, supporting theoretical predictions that Muller's ratchet contributes to mutation accumulation in asexual lineages.

The cloud forest harbors the highest amphibian diversity in Mexico, particularly among plethodontid salamanders. However, the expansion of agricultural and cattle ranching activities has significantly impacted this ecosystem and their native species. Beyond direct effects on cloud forest-dwelling species, effects of land-use change on free-living and salamander skin associated bacterial assemblages are underexplored in the cloud forest and in plethodontid salamanders specifically. This study examines how historical land-use changes may influence environmental and salamander skin bacterial communities, focusing on two types of previous land-use and six sympatric plethodontid salamanders from the cloud forest. Furthermore, we explored the presence of the pathogenic fungus Batrachochytrium dendrobatidis ( Bd ), due to its potential interaction with salamander skin bacterial communities. We found that skin bacterial communities varied with land-use history: in habitats formerly used for agriculture salamanders exhibited higher bacterial diversity, and communities’ dispersion varied depending on the previous land-use. We found a very low Bd prevalence throughout the study area. Our findings suggest that bacterial communities associated with the skin of plethodontid salamanders may be influenced by land-use history in cloud forest fragments.

Caves are a challenging environment for many organisms to inhabit, and many cave-dwelling animals are endemic to particular cave systems. Microorganisms in caves have been shown to have a high biosynthetic capacity, likely as a result of intense biological interactions to deal with resource scarcity. Although cave salamanders have been studied extensively in other parts of the world, they have received relatively little attention in Mexico. Declines of some cave-dwelling species may be due to outbreaks of fungal disease, and a better understanding of their cutaneous microbiome could help with future conservation efforts in the face of disease outbreaks. We characterized the cutaneous microbiome of 11 cave-dwelling Mexican salamanders and their relatives from surface environments using high-throughput 16S amplicon sequencing. We expected cave salamanders to have a more diverse microbiome containing more bacteria with potential antifungal capacity compared to forest salamanders. We also estimated networks of associations between bacteria to test the hypothesis that there are more positive associations in caves. Finally, we used a bioinformatic approach to see if bacteria in caves potentially have more metabolic pathways associated with microbial communication as a result of more intense biological interactions in caves. Although we do not find higher skin bacterial diversity in caves compared to forests, we do find differences in microbiome composition between environments, more positive associations between bacteria, and a slightly higher number of metabolic pathways associated with microbial communication in caves. Our results provide some support for an impact of the cave environment on the skin microbiome of Mexican salamanders.

Transposable elements (TEs) compose a substantial proportion of the largest eukaryotic genomes. TE diversity has been hypothesized to be negatively correlated with genome size, yet empirical demonstrations of such a relationship in a phylogenetic context are largely lacking. Furthermore, the most abundant type of TEs in genomes varies across groups, and it is not clear if there are patterns of TE activity consistent with genome size among different taxa with large genome sizes. We use low-coverage sequencing of 16 species of Neotropical salamanders, which vary ∼7-fold in genome size, to estimate TE relative abundance and diversity for each species. We also compare the divergence of copies of each TE superfamily to estimate patterns of TE activity in each species. We find a negative relationship between TE diversity and genome size, which is consistent with the hypothesis that either competition among TEs or reduced selection against ectopic recombination may result in lower diversity in the largest genomes. We also find divergent activity patterns in the largest versus the smallest genomes, suggesting that the history of TE activity may explain differences in genome size. Our results suggest that both TE diversity and relative abundance may be predictable, at least within taxonomic groups.

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.

Genetic diversity is the raw material of evolution, yet the reasons why it varies among species remain poorly understood. While studies at deeper phylogenetic scales point to the influence of life history traits on genetic diversity, it appears to be more affected by population size but less predictable at shallower scales. We used proxies for population size, mutation rate, direct selection, and linked selection to test factors affecting genetic diversity within a diverse assemblage of Neotropical salamanders, which vary widely for these traits. We estimated genetic diversity of noncoding loci using ddRADseq and coding loci using RNAseq for an assemblage of Neotropical salamanders distributed from northern Mexico to Costa Rica. Using ddRADseq loci, we found no significant association with genetic diversity, while for RNAseq data we found that environmental heterogeneity and proxies of population size predict a substantial portion of the variance in genetic diversity across species. Our results indicate that diversity of coding loci may be more predictable than that of noncoding loci, which appears to be mostly unpredictable at shallower phylogenetic scales. Our results suggest that coding loci may be more appropriate for genetic diversity estimates used in conservation planning because of the lack of any association between the variables we used and genetic diversity of noncoding loci.

We describe a new species of plethodontid salamander of the genus Pseudoeurycea from the Sierra de Zongolica, Veracruz, Mexico. The new species is distinguished from all other species in the genus by morphological and genetic features and by coloration. Based on a mtDNA phylogeny, the new species belongs to the Pseudoeurycea juarezi group and is most closely related to P. ruficauda from the Sierra Mazateca in northern Oaxaca. The newly described salamander increases the number of species of plethodontid salamanders from Veracruz to 43 and those recognized from Mexico to 140.

Host microbial communities are increasingly seen as an important component of host health. In amphibians, the first land vertebrates that are threatened by a fungal skin disease globally, our understanding of the factors influencing the microbiome of amphibian skin remains incomplete because recent studies have focused almost exclusively on bacteria, and little information exists on fungal communities associated with wild amphibian species. In this study, we describe the effects of host phylogeny, climate, geographic distance, and infection with a fungal pathogen on the composition and structure of bacterial and fungal communities in seven tropical salamander species that occur in the Trans-Mexican Volcanic Belt of Central Mexico. We find that host phylogenetic relatedness is correlated with bacterial community composition while a composite climatic variable of temperature seasonality and precipitation is significantly associated with fungal community composition. We also estimated co-occurrence networks for bacterial and fungal taxa and found differences in the degree of connectivity and the distribution of negative associations between the two networks. Our results suggest that different factors may be responsible for structuring the bacterial and fungal communities of amphibian skin and that the inclusion of fungi in future studies could shed light on important functional interactions within the microbiome.

Emergent infectious disease caused by the fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) represents one of the major causes of biodiversity loss in amphibians. While Bd has affected amphibians worldwide, Bsal remains restricted to Asia and Europe, but also could be a major threat for salamanders in the Western hemisphere, including the 320 bolitoglossine species described. Here, we predict the suitable areas for Bsal in the Neotropics and assess its potential impact on bolitoglossine diversity. For this, we determined the geographic patterns of taxonomic, phylogenetic, and functional diversity for bolitoglossines and modeled the potential distribution of Bsal in the Neotropics. We identified which species and regions could be at risk from an eventual introduction of Bsal in the region, quantified the degree of overlap between regions of high diversity and the suitable conditions for the pathogen, and considered species IUCN Red List status, and geographic range size. We found that regions of high taxonomic, phylogenetic, and functional diversity are concentrated in the Trans‐Mexican Volcanic Belt, Sierra Madre Oriental, the southern portion of Sierra Madre del Sur and the mountains of Oaxaca in México, as well as the Chiapan‐Guatemalan highlands, and the Cordilleras of Costa Rica and Panama. Alarmingly, the regions of high diversity for bolitoglossines and over 75% of the ranges of the more threatened species could be affected by Bsal. Given the unknown vulnerability of these species, we strongly recommend measures to avoid the introduction of Bsal in the continent.Abstract in Spanish is available with online material.

The fungal pathogenBatrachochytrium dendrobatidis(Bd) is implicated in global mass die-offs and declines in amphibians. In Mesoamerica, theBdepidemic wave hypothesis is supported by detection ofBdin historic museum specimens collected over the last century, yet the timing and impact of the early stages of the wave remain poorly understood.Chiropterotriton magnipes, the only obligate troglodytic Neotropical salamander, was abundant in its small range in the decade following its description in 1965, but subsequently disappeared from known localities and was not seen for 34 years. Its decline is roughly coincident with that of other populations of Neotropical salamanders associated with the invasion and spread ofBd. To determine the presence and infection intensity ofBdonC. magnipesand sympatric amphibian species (which are alsoBdhosts), we used a noninvasive sampling technique and qPCR assay to detectBdon museum specimens ofC. magnipescollected from 1952 to 2012, and from extant populations ofC. magnipesand sympatric species of amphibians. We also tested for the presence of the recently discoveredBatrachochytrium salamandivorans(Bsal), another fungal chytridiomycete pathogen of salamanders, using a similar technique specific forBsal. We did not detectBdin populations ofC. magnipesbefore 1969, whileBdwas detected at low to moderate prevalence just prior to and during declines. This pattern is consistent withBd-caused epizootics followed by host declines and extirpations described in other hosts. We did not detectBsalin any extant population ofC. magnipes. We obtained one of the earliest positive records of the fungus to date in Latin America, providing additional historical evidence consistent with theBdepidemic wave hypothesis. Genotyping results show that at least one population is currently infected with the Global Panzootic Lineage ofBd, but our genotyping of the historical positive samples was unsuccessful. The lack of large samples from some years and the difficulty in genotyping historical Bd samples illustrate some of the difficulties inherent in assigning causality to historical amphibian declines. These data also provide an important historical baseline for actions to preserve the few known remaining populations ofC. magnipes.