Phylogeography of the Volcano Rabbit (Romerolagus diazi): the Evolutionary History of a Mountain Specialist Molded by the Climatic-Volcanism Interaction in the Central Mexican Highlands

Phylogeography and taxonomy of Coleonyx elegans Gray 1845 (Squamata: Eublepharidae) in Mesoamerica: The Isthmus of Tehuantepec as an environmental barrier

Population divergence leading to speciation is often explained by physical barriers causing allopatric distributions of historically connected populations. Environmental barriers have increasingly been shown to cause population divergence through local adaptation to distinct ecological characteristics. In this study, we evaluate population structuring and phylogeographic history within the Yucatán banded gecko Coleonyx elegans Gray 1845 to assess the role of both physical and environmental barriers in shaping the spatio-genetic distribution of a Mesoamerican tropical forest taxon. We generated RADseq and multi-locus Sanger datasets that included sampling across the entire species' range. Results find support for two distinct evolutionary lineages that diverged during the late Pliocene and show recent population expansions. Furthermore, these genetic lineages largely align with subspecies boundaries defined by morphology. Several mountain ranges identified as phylogeographic barriers in other taxa act as physical barriers to gene flow between the two clades. Despite the absence of a physical barrier between lineages across the lowland Isthmus of Tehuantepec, no introgression was observed. Here, a steep environmental cline associated with seasonality of precipitation corresponds exactly with the distributional limits of the lineages, whose closest samples are only 30 km apart. The combination of molecular and environmental evidence, and in conjunction with previous morphological evidence, allows us to reassess the current taxonomy in an integrative framework. Based on our findings, we elevate the previously recognized subspecies from the Pacific versant, the Colima banded gecko C. nemoralis Klauber 1945, to full species status and comment on conservation implications.

Phylogeography supports lineage divergence for an endemic rattlesnake (Crotalus ravus) of the Neotropical montane forest in the Trans-Mexican Volcanic Belt

The formation of the Trans-Mexican Volcanic Belt (TMVB) and Pleistocene climatic fluctuations have been shown to influence the diversification of lineages and species distributed throughout central Mexico. In some taxa, however, evidence of lineage diversification is not easily recognized, as often is the case in reptiles. Here we present a phylogeographic study on a Mexican endemic rattlesnake species (Crotalus ravus), with the aim of understanding how distinct lineages are distributed across the TMVB. Genetic (mtDNA) and genomic (ddRADseq) data were generated from samples across the species’ range to evaluate phylogeographic structure, estimate phylogenetic relationships and divergence times, and perform environmental niche modeling (ENM). Both datasets recover strong phylogeographic structuring of two distinct lineages on an east-west axis, with an estimated Pleistocene divergence (~1.47 Myr). The ENM suggest that the distribution of the two lineages experienced expansion and reduction events throughout recent evolutionary time. We attribute the diversification of C. ravus lineages to geological events associated with the formation of the TMVB, as well as Quaternary climate changes, both of which have been previously recognized in co-distributed taxa in the TMVB. This work emphasizes the existence of cryptic diversification processes in a morphologically conserved species distributed in a region of complex climatic and orogenic heterogeneity.

Legacy of supervolcanic eruptions on population genetic structure of brown kiwi

Supervolcanoes are volcanoes capable of mega-colossal eruptions that emit more than 1,000 km³ of ash and other particles.¹ The earth's most recent mega-colossal eruption was the Oruanui eruption of the Taupo supervolcano 25,580 years before present (YBP) on the central North Island of New Zealand.² This eruption blanketed major swaths of the North Island in thick layers of ash and igneous rock,^2,3 devastating habitats and likely causing widespread population extinctions.^4-7 An additional devastating super-colossal eruption (>100 km³) of the Taupo supervolcano occurred approximately 1,690 YBP.⁸ The impacts of such massive but ephemeral natural disasters on contemporary population genetic structure remain underexplored. Here, we combined data for 4,951 SNPs with spatially explicit demographic and coalescent models within an approximate Bayesian computation framework to test the drivers of genetic structure in brown kiwi (Apteryx mantelli). Our results strongly support the importance of eruptions of the Taupo supervolcano in restructuring pre-existing geographic patterns of population differentiation and genetic diversity. Range shifts due to climatic oscillations-a frequent explanation for genetic structure⁹-are insufficient to fully explain the empirical data. Meanwhile, recent range contraction and fragmentation due to historically documented anthropogenic habitat alteration adds no explanatory power to our models. Our results support a major role for cycles of destruction and post-volcanic recolonization in restructuring the population genomic landscape of brown kiwi and highlight how ancient and ephemeral mega-disasters may leave a lasting legacy on patterns of intraspecific genetic variation.

The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico

BACKGROUND

The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species.

METHODS AND RESULTS

This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs.

CONCLUSIONS

This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.

Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi)

Background

The volcano rabbit is the smallest lagomorph in Mexico, it is monotypic and endemic to the Trans-Mexican Volcanic Belt. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Romerolagus diazi consumes large amounts of grasses, seedlings, shrubs, and trees. Pines and oaks contain tannins that can be toxic to the organisms which consume them. The volcano rabbit microbiota may be rich in bacteria capable of degrading fiber and phenolic compounds.

Methods

We obtained the fecal microbiome of three adults and one young rabbit collected in Coajomulco, Morelos, Mexico. Taxonomic assignments and gene annotation revealed the possible roles of different bacteria in the rabbit gut. We searched for sequences encoding tannase enzymes and enzymes associated with digestion of plant fibers such as cellulose and hemicellulose.

Results

The most representative phyla within the Bacteria domain were: Proteobacteria, Firmicutes and Actinobacteria for the young rabbit sample (S1) and adult rabbit sample (S2), which was the only sample not confirmed by sequencing to correspond to the volcano rabbit. Firmicutes, Actinobacteria and Cyanobacteria were found in adult rabbit samples S3 and S4. The most abundant phylum within the Archaea domain was Euryarchaeota. The most abundant genera of the Bacteria domain were Lachnoclostridium (Firmicutes) and Acinetobacter (Proteobacteria), while Methanosarcina predominated from the Archaea. In addition, the potential functions of metagenomic sequences were identified, which include carbohydrate and amino acid metabolism. We obtained genes encoding enzymes for plant fiber degradation such as endo 1,4 β-xylanases, arabinofuranosidases, endoglucanases and β-glucosidases. We also found 18 bacterial tannase sequences.

Factors affecting presence and relative abundance of the Endangered volcano rabbit Romerolagus diazi, a habitat specialist

Habitat specialists are particularly vulnerable to extinction when habitat conditions are altered. Information on the habitat use of such species is thus important because it provides insight into factors that influence distribution and abundance, which is crucial for conservation. Here, we aimed to identify factors that influence the patterns of presence and abundance of the Endangered volcano rabbit Romerolagus diazi, a rare leporid with a patchy distribution. Through exhaustive sampling of its range in the Sierra Chichinautzin and Sierra Nevada volcanic fields, Mexico, and using generalized linear models, we found that the probability of patch occupancy was higher where bunchgrass cover exceeded 75%, rock cover exceeded 5%, no cattle grazing was observed and human settlements were at least 7 km away. Patches with greater relative abundance were those with similar characteristics, but located at elevations > 3,600 m, and with rock cover < 15%. Cattle grazing was identified as a major threat to local populations of the volcano rabbit, particularly in the Sierra Chichinautzin. Because of the significance of bunchgrasses for this species, the protection of the mountain grasslands is required in both volcanic fields.