Genetic diversity and demography of two endangered captive pronghorn subspecies from the Sonoran Desert

Climatically robust multiscale species distribution models to support pronghorn recovery in California

We combined two climate-based distribution models with three finer-scale suitability models to identify habitat for pronghorn recovery in California now and into the future. We used a consensus approach to identify areas of suitable climate now and future for pronghorn in California. We compared the results of climate models from two separate hypotheses about their historical ecology in the state. Under the migration hypothesis, pronghorn were expected to be limited climatically by extreme cold in winter and extreme heat in summer; under the niche reduction hypothesis, historical pronghorn of distribution would have better represented the climatic limitations of the species. We combined occurrences from GPS collars distributed across three populations of pronghorn in the state to create three distinct habitat suitability models: (1) an ensemble model using random forests, Maxent, classification and regression Trees, and a generalized linear model; (2) a step selection function; and (3) an expert-driven model. We evaluated consensus among both the climate models and the suitability models to prioritize areas for, and evaluate the prospects of, pronghorn recovery. Climate suitability for pronghorn in the future depends heavily on model assumptions. Under the migration hypothesis, our model predicted that there will be no suitable climate in California in the future. Under the niche reduction hypothesis, by contrast, suitable climate will expand. Habitat suitability also depended on the methods used, but areas of consensus among all three models exist in large patches throughout the state. Identifying habitat for a species which has undergone extreme range collapse, and which has very fine scale habitat needs, presents novel challenges for spatial ecologists. Our multimethod, multihypothesis approach can allow habitat modelers to identify areas of consensus and, perhaps more importantly, fill critical knowledge gaps that could resolve disagreements among the models. For pronghorn, a better understanding of their upper thermal tolerances and whether historical populations migrated will be crucial to their potential recovery in California and throughout the arid Southwest.

Ruminant inner ear shape records 35 million years of neutral evolution

Extrinsic and intrinsic factors impact diversity. On deep-time scales, the extrinsic impact of climate and geology are crucial, but poorly understood. Here, we use the inner ear morphology of ruminant artiodactyls to test for a deep-time correlation between a low adaptive anatomical structure and both extrinsic and intrinsic variables. We apply geometric morphometric analyses in a phylogenetic frame to X-ray computed tomographic data from 191 ruminant species. Contrasting results across ruminant clades show that neutral evolutionary processes over time may strongly influence the evolution of inner ear morphology. Extant, ecologically diversified clades increase their evolutionary rate with decreasing Cenozoic global temperatures. Evolutionary rate peaks with the colonization of new continents. Simultaneously, ecologically restricted clades show declining or unchanged rates. These results suggest that both climate and paleogeography produced heterogeneous environments, which likely facilitated Cervidae and Bovidae diversification and exemplifies the effect of extrinsic and intrinsic factors on evolution in ruminants.

The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act

More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.

The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn

Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are essential for conservation. The Peninsular pronghorn (Antilocapra americana peninsularis) is an endangered pronghorn subspecies that is almost entirely held in captivity. Captive breeding has increased the number of pronghorns from 25 founders in 1997 to around 700 individuals today, but it is unclear how the genetic diversity of the captive herd may have changed over time. We therefore generated and analysed data for 16 microsatellites spanning 2009-2021. We detected a decline in heterozygosity and an increase in the proportion of inbred individuals over time. However, these trends appear to have been partially mitigated by a genetically informed breeding management attempt that was implemented in 2018. We also reconstructed the recent demographic history of the Peninsular pronghorn, revealing two sequential population declines putatively linked to the desertification of the Baja California peninsula around 6000 years ago, and hunting and habitat loss around 500 years ago, respectively. Our results provide insights into the genetic diversity of an endangered antelope and indicate the potential for genetically informed management to have positive conservation outcomes.

Pronghorn population genomics show connectivity in the core of their range

Preserving connectivity in the core of a species' range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that pronghorn populations declined significantly in the early 1900s, have only partially recovered, and are experiencing modern threats from landscape modification, conserving connectivity among populations is important for their long-term persistence in North America. To assess the genetic structure and diversity of pronghorn in the core of their range, we genotyped 4,949 genome-wide single-nucleotide polymorphisms and 11 microsatellites from 398 individuals throughout the state of Wyoming. We found no evidence of genetic subdivision and minimal evidence of isolation by distance despite a range that spans hundreds of kilometers, multiple mountain ranges, and three interstate highways. In addition, a rare variant analysis using putatively recent mutations found no genetic division between pronghorn on either side of a major highway corridor. Although we found no evidence that barriers to daily and seasonal movements of pronghorn impede gene flow, we suggest periodic monitoring of genetic structure and diversity as a part of management strategies to identify changes in connectivity.