Search for: All records

The genomic characteristics of adaptively radiated groups could contribute to their high species number and ecological disparity, by increasing their evolutionary potential. Here, we explored the genomic variation of Anolis lizards, focusing on three species with distinct phenotypes: A. auratus, one of the species with the longest tail; A. frenatus, one of the largest species; and A. carolinensis, one of the species that inhabits the coldest environments. We assembled and annotated two new chromosome-level reference genomes for A. auratus and A. frenatus, and compared them with the available genomes of A. carolinensis and A. sagrei. We evaluated the presence of structural rearrangements, quantified the density of repeat elements, and identified potential signatures of positive selection in coding and regulatory regions. We detected substantial rearrangements in scaffolds 1, 2 and 3 of A. frenatus different from the other species, in which the rearrangement breakpoints corresponded to hotspots of developmental genes. Further, we detected an accumulation of repeats around key developmental genes in anoles and phrynosomatid outgroups. Finally, coding sequences and regulatory regions of genes relevant to development and physiology showed variation that could be associated with the unique phenotypes of the analyzed species. Our results show examples of the hierarchical genomic variation within anoles, that could provide the substrate that promoted phenotypic disparity and contributed to their adaptive radiation. 

Uta stansburiana are an emerging model system for studying sexual selection, polymorphism, and the evolution of pace-of-life syndromes (POLS) whose distribution covers variable environments and a wide latitudinal gradient. POLS are suites of traits causing variation of life history along a slow maturing-fast maturing continuum. We present a high-quality chromosome-level reference genome for U. stansburiana and pair it with RNA-seq gene expression data to demonstrate, for the first time, the molecular basis for pace-of-life differences between locations with higher and lower climate seasonality and sexual size dimorphism (SSD). Our assembly is 2.1 Gbp, has scaffold N50 of 320 Mbp, includes 104 scaffolds, and has an L50 of 3. The assembly comprises six macrochromosomes and 11 microchromosomes. We annotated 20,350 genes for the assembly and found a repeat element composition of 49.23%, similar to work in other phrynosomatid lizards. RNA-seq gene expression data demonstrate expression differences in genes associated with pace-of-life differences including those related to stress, sexual reproduction, and cell proliferation/carcinogenesis between different environments. Our results provide the first differential gene expression evidence of environmentally-mediated pace-of-life processes related to different degrees of SSD in U. stansburiana and demonstrate the utility of RNA-seq gene expression data in detecting POLS. 

Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species' responses to climatic changes between Last Glacial Maximum (LGM) and present day. We built ecological niche models for genetic groups within 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Significant niche divergence was detected for all clades within species, along with significant differences in the niche breadth and area of distribution between northern and southern clades. We quantified habitat quantity from the distribution models, and most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species. Our results suggest that changes in habitat quantity and quality can affect organismal responses independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested from our models. 

We develop a conceptual framework for geo-evolutionary feedbacks which de- scribes the mutual interplay between landscape change and the evolution of traits of organisms residing on the landscape, with an emphasis on contempo- rary timeframes. Geo-evolutionary feedbacks can be realized via the direct evo- lution of geomorphic engineering traits or can be mediated by the evolution of trait variation that affects the population size and distribution of the specific geo- morphic engineering organisms involved. Organisms that modify their local envi- ronments provide the basis for patch-scale geo-evolutionary feedbacks, whereas spatial self-organization provides a mechanism for geo-evolutionary feedbacks at the landscape scale. Understanding these likely prevalent geo- evolutionary feedbacks, that occur at timescales similar to anthropogenic cli- mate change, will be essential to better predict landscape adaptive capacity and change. 

Abstract Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334–127 Mb) representing macrochromosomes and 8 small scaffolds (63–22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic. 

Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents’ prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution. 

Abstract There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.