Geology topics

Greer A. Dolby

Publications and source records attributed to Greer A. Dolby.

4 recordsLinked to original sources

USGS2023

Chromosome-level genome assembly of the blacktail brush lizard, Urosaurus nigricaudus, reveals dosage compensation in an endemic lizard

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.

Genome Biology and Evolution↗

USGS2022

Integrating Earth–life systems: A geogenomic approach

For centuries, scientists have recognized and worked to understand how Earth’s mutable landscape and climate shape the distribution and evolution of species. Here, we describe the emerging field of geogenomics, which uses the reciprocal and deep integration of geologic, climatic, and population genomic data to define and test cause–effect relationships between Earth and life at intermediate spatial and temporal scales (i.e., the mesoscale). Technological advances now power the detailed reconstruction of landscape and evolutionary histories, but transdisciplinary collaborations and new quantitative tools are needed to better integrate Earth–life data. Geogenomics can help build a more unified theory and characterize the boundary conditions under which geologic and climatic processes generate new biodiversity, how species’ responses differ, and why.

Trends in Ecology & Evolution↗

USGS2020

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii

The immune system of ectotherms, particularly non-avian reptiles, remains poorly characterized regarding the genes involved in immune function, and their function in wild populations. We used RNA-Seq to explore the systemic response of Mojave desert tortoise ( Gopherus agassizii ) gene expression to three levels of Mycoplasma infection to better understand the host response to this bacterial pathogen. We found over an order of magnitude more genes differentially expressed between male and female tortoises (1,037 genes) than differentially expressed among immune groups (40 genes). There were 8 genes differentially expressed among both variables that can be considered sex-biased immune genes in this tortoise. Among experimental immune groups we find enriched GO biological processes for cysteine catabolism, regulation of type 1 interferon production, and regulation of cytokine production involved in immune response. Sex-biased transcription involves iron ion transport, iron ion homeostasis, and regulation of interferon-beta production to be enriched. More detailed work is needed to assess the seasonal response of the candidate genes found here. How seasonal fluctuation of testosterone and corticosterone modulate the immunosuppression of males and their susceptibility to Mycoplasma infection also warrants further investigation, as well as the importance of iron in the immune function and sex-biased differences of this species. Finally, future transcriptional studies should avoid drawing blood from tortoises via subcarapacial venipuncture as the variable aspiration of lymphatic fluid will confound the differential expression of genes.

PLoS ONE↗

USGS2020

Global physical controls on estuarine habitat distribution during sea levelchange: Consequences for genetic diversification through time

Determining the extrinsic (physical) factors controlling speciation and diversification of species through time is of key interest in paleontology and evolutionary biology. The role of sea-level change in shaping species richness patterns of marginal marine species has received much attention, but with variable conclusions. Recent work combining genetic data and Geographical Information Systems (GIS)-based habitat modeling yielded a framework for how geomorphology of continental margins mediates genetic connectivity of populations during sealevel change. This approach may ultimately yield insights on how distinct lineages, species, and biodiversity accumulate in coastal settings. Here, we expand this GIS work globally to different geomorphic settings to model estuarine habitat in a larger geographic framework and test how tectonic setting, oceanographic setting, climate, and margin age affect habitat distribution during sea-level change. In addition, independent of estuaries we explore paleobiologic (e.g. Olsson, 1961) and neontolologic effects of sea-level change on evolution, and test the relation between overall shelf area and species richness using data of 1721 fish species. We find 82% global reduction of estuarine habitat abundance at lowstand relative to highstand, and find large habitats change in size much more than small habitats. Consistent with prior work, narrow continental margins have significantly less habitat at highstand and lowstand than wide margins, and narrow margins significantly associate with fore-arc settings, effectively linking tectonic setting to habitat abundance. Surprisingly, narrow margins host greater species richness, a finding which violates the canonical species-area relation. This finding can be explained if: 1) the physical isolation imposed by narrow margins facilitates the formation of new species over time; 2) the sizestability of small habitats, which disproportionately occur on narrow margins, accumulate and retain species extirpated in the more variable habitats on wide margins; or 3) the smaller habitats on narrow margins facilitate greater species richness through greater habitat heterogeneity. These results are generally at odds with prior interpretations, but the combination of richness data and population genetic principles offer a different perspective on these long-studied questions. Finally, we emphasize that the nuance of Pleistocene-Holocene sea level oscillations should be more explicitly considered in genetic studies.

Global and Planetary Change↗