Geology topics

Robert D. Cooper

Publications and source records attributed to Robert D. Cooper.

3 recordsLinked to original sources

USGS2026

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

Journal of Heredity↗

USGS2026

A chromosome-level genome assembly of a vernal pool specialist amphibian, the Western Spadefoot, Spea hammondii

We assembled and annotated a chromosome-level reference genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (QV = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This reference genome, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

BioRxiv↗

USGS2017

Climate change and collapsing thermal niches of Mexican endemic reptiles

Recent climate change should result in expansion of species to northern or high elevation range margins, and contraction at southern and low elevation margins due to extinction. Climate models predict dramatic extinctions and distributional shifts in the next century, but there are few ground-truths of these dire forecasts leading to uncertainty in predicting extinctions due to climate change. Previously, we reported on recent extinctions of Mexican Sceloporus lizards by comparing recent surveys to historical distributional records for 48 species at 200 sites. We also ground-truthed extinctions on five continents across 8 lizard families by comparing observed and predicted extinctions from an eco-physiological species distribution model and obtained a high R 2 of 0.72 (1, 2). Here, we derive more detailed predictions for 15 terrestrial reptile families and 142 species for the Mexican and California Biogeographic provinces using all known museum occurrence records, and detailed measures on eco-physiology. We adopt the eco-physiological model of extinction developed earlier but use a species-specific model. We predict massive and rapid extinctions of 22% of the reptile populations in Mexico within the next 50 years. We also predict that 3 of 15 reptile families, all three endemic to the Mexican and Californian biogeographic provinces, will go extinct by 2070, the hallmark of the beginnings of a mass extinction event. However, extinctions may be attenuated by forest cover and by presence of montane environments in contemporary ranges. We describe impacts of altitude on three species (Gopherus morafkai, G. evgoodei, and Gambelia sila) to illustrate regional management strategies (AZ-Mexico, Sinoloa, CA) for reserves in tandem with global strategies of CO2 limits that might limit climate impacts. By carefully selecting new montane preserves adjacent to desert and tropical forest habitats, and by implementing global controls on atmospheric CO2 emissions, extinctions may be reduced to less than 11% of species and only a single reptile family.

Report↗