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

Abstract

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.

Contrasting management paradigms for pronghorn in the arid Southwest and their northern range: a review

“…Repeated analysis has supported the differentiation of Peninsular and Sonoran subspecies from the American (Klimova et al 2014, Hahn et al 2020, 2021). Unsurprisingly, populations that have undergone recent bottlenecks have lost genetic diversity and become more genetically distinct from nearby populations; this pattern has been documented in Sonoran (Stephen et al 2005 a , Klimova et al 2014, Hahn et al 2021) and Peninsular (Klimova et al 2014, 2022) semi‐captive populations, in populations on the National Bison Range in Montana (Dunn et al 2011), and in a re‐introduced population in Oregon (Stephen et al 2005 b ). Lee et al (1989) documented low genetic diversity in Trans‐Pecos populations of pronghorn, and they suggested that the genetic structure of the herds were confused by multiple, poorly documented translocation events from outside of the region.…”

Population genomics and distribution modeling revealed the history and suggested a possible future of the endemic Agave aurea (Asparagaceae) complex in the Baja California Peninsula

“…For example, Yucca schidigera populations in the BCP ( F ST = 0.067), as well as the endemic Yucca capensis ( F ST = 0.02) (De la Rosa‐Conroy et al., 2019 ; Luna‐Ortiz et al., 2021 ). Moreover, two subspecies of Agave cerulata from the north of the BCP also showed low genetic differentiation ( F ST = 0.098; Navarro‐Quezada et al., 2003 ), as did populations of Agave palmeri in Arizona ( F ST = 0.04; Lindsay et al., 2018 ), Agave angustifolia , in the Sonora state of Mexico ( F ST = 0.076; Klimova, Gutiérrez‐Rivera, et al., 2022 ), and Agave potatorum in southern Mexico ( F ST = 0.08; Ruiz‐Mondragón et al., 2023 ).…”

“…Genomic DNA from 98 individuals of Agave aurea sensu Webb and Starr ( 2015 ) was extracted using a modified hexadecyltrimethylammonium bromide (CTAB) protocol from the frozen leaf tissue disrupted with liquid nitrogen (Doyle & Doyle, 1987 ; Klimova, Gutiérrez‐Rivera, et al., 2022 ; Klimova, Mondragón, et al., 2022 ). The DNA quality was checked on a 1% agarose gel.…”

“…In addition to the uncertainty in species delimitation, there is a growing concern for the conservation of the flora and fauna of the BCP (Benavides et al., 2020 ; Dávila et al., 2022 ; Klimova, Gutiérrez‐Rivera, et al., 2022 ; Klimova, Mondragón, et al., 2022 ; Riemann & Ezcurra, 2005 ; Vanderplank et al., 2014 ). Like other arid areas around the globe, Baja California has been heavily influenced by anthropogenic disturbances, such as overgrazing by free‐roaming livestock, off‐road recreational vehicles, agriculture, and climate change (Riemann & Ezcurra, 2005 ; Wehncke et al., 2014 ).…”

Evaluation of the Impact of Population Management on the Genetic Parameters of Selected Spiral-Horned Antelopes

“…Population management in zoos has included an explicit focus on genetic diversity for over twenty years, with methods based on pedigree data proving efficient in mitigating the diversity loss [23][24][25][26][27][28]. However, challenges often arise when pedigree records are incomplete or inaccurate [29,30].…”