Search for: All records

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. 

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. 

Understanding the causes of differential divergence patterns in nature is a longstanding challenge in evolutionary biology. While external factors such as landscape change or selective pressures have been commonly proposed as the main drivers of differentiation, the intrinsic features of… 

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. 

For nearly 30 years, biologists have documented a striking pattern of intra-species genetic divergence on the Baja California peninsula in dozens of disparate species. Evolutionary theory predicts that when such a pattern is shared among species the cause is extrinsic (e.g., environmental, climatic, physiographic, geological). The leading hypothesis within biological literature has been that genetic divergence was facilitated by flooding across the central peninsula by a seaway between ~3-1 Ma, resulting in separation of northern and southern populations. However, new detailed geologic mapping from the Baja GeoGenomics consortium reveals evidence for continuous terrestrial environments during the last ~30 Myr in a ≥40-km-wide ~E-W region of the central peninsula that straddles the modern-day crest, conclusively refuting the seaway hypothesis. Through integration of tectonic, volcanic, and sedimentological evidence with genomic (DNA) and gene expression (RNA) data for plants and animals, we are developing a new working model for Earth-life evolution on the peninsula over the last ~5 Myr. In this model, rift-related uplift drives the growth and dissection of topography, causing increased microenvironmental heterogeneity that populations differentially adapted to in the north and south. This is evidenced by widespread, statistically significant niche divergence in populations between northern and southern Baja in 21 studied taxa. This pattern is supported by strong differences in gene expression in northern and southern populations of two lizard species, particularly in genes relating to metabolism, which may indicate different diet or energy requirements between the regions. Habitats in the north and south then shifted due to glacial and interglacial periods, indicated by hindcasting the estimated niche conditions of those 21 taxa. With ongoing analyses, we expect to find genomic signatures of differential natural selection and adaptation within these species due in part to monsoon-driven rainfall differences. The significance of this work is twofold: it demonstrates the importance of incorporating geological data into evolutionary hypotheses and it cautions how mis-assigning cause-effect relationships in individual Earth-life systems can bias our fundamental understanding of how Earth processes shape biological evolution writ large.