Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf

Abstract

The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.

Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole‐genome sequencing

“…Our results are in line with previous studies showing that isolated and diminished wolf populations have a higher chance of hybridising with closely related species, especially dogs (Ballard et al, 2003; Ciucani et al, 2022; Niemann et al, 2021; Phillips et al, 2003; Randi et al, 2001; vonHoldt et al, 2022). Our data revealed that the HKW is admixed with dogs, with the Shar Pei breed being the most likely source of ancestry contributing to the genetic composition of this specimen.…”

“…The dataset used for this study includes 74 canid whole‐genomes: One Andean fox ( Lycalopex culpaeus ) (Auton et al, 2013), two coyotes ( Canis latrans ) (Gopalakrishnan et al, 2018; vonHoldt et al, 2022), 51 wolves ( C. lupus ) (Fan et al, 2016; Freedman et al, 2014; Hennelly et al, 2021; Niemann et al, 2021; Ramos‐Madrigal et al, 2021; Sinding et al, 2018, 2020; vonHoldt et al, 2016; Wang et al, 2013, 2016; Zhang et al, 2014), and 20 dogs (Auton et al, 2013; Decker et al, 2015; Freedman et al, 2014; Kim et al, 2012; Kolicheski et al, 2017; Lindblad‐Toh et al, 2005; Marchant et al, 2017; Marsden et al, 2016; Metzger et al, 2017; Sinding et al, 2020; Wang et al, 2016) Among the wolf samples, 40 are reference genomes mainly representing Asian populations; five correspond to Pleistocene wolves from Siberia, 10 correspond to wolves resequenced for this study representing wolf populations in Asia, and two are the Korean wolves (a modern captive wolf [PZW] from the Seoul Grand Park in South Korea, and a 20th century mounted Korean wolf [HKW] from the Kyungpook University Museum; Figure S9). Finally, all dog genomes included here have been previously published and they were selected to mainly represent Asian breeds (Table S2).…”

Integrating genomics and conservation to safeguard plant diversity

“…Some of the genetic diversity may be even maintained in the hybrids formed, where they may be recovered using genomic tools. A recent genomic study on red wolfs in North America confirmed this possibility (vonHoldt et al, 2022). Related evidence was also reported for hybrids formed in the threatened asteroid genus Commidendrum —an endemic to the endangered flora of the Atlantic St. Helena Island (Gray et al, 2017).…”

“…In some cases, these efforts may require genetic rescue, sometimes even using closely related species (Ralls et al, 2020; Whiteley et al, 2015). Reference genomes have now been employed to support the protection of threatened vertebrates via breeding programs or related conservation programs such as the giant panda (Li et al, 2010), the Tasmanian devil (Brandies et al, 2019), Chinese pangolins (Wang et al, 2022), Aldabra giant tortoise (Çilingir et al, 2022), and red wolf (vonHoldt et al, 2022), but have not been widely used in plants until recently. This bias may be partly explained by less promotion of charismatic species such as those animals mentioned above, but this trend is arguably challenged by recent efforts to promote plant conservation by focusing on iconic plants including the living fossil Ginkgo (Liu et al, 2021), palms (Bellot et al, 2022), conifers such as Coast Redwood and Giant sequoia (De La Torre et al, 2021; Neale et al, 2021; Scott et al, 2020), island endemics (Hamabata et al, 2019), and rhododendrons (Ma et al, 2021).…”

Genomic-guided conservation actions to restore the most endangered conifer in the Mediterranean Basin

“…Notably, two adult Sicilian firs exhibited indications of coancestry with silver firs in the PCA, suggesting historical introgression of anthropical origin due to plantations from at least one century as occurred in other tree species (Vanden Broeck et al 2005; Meirmans et al 2014; Scotti-Saintagne et al 2023). Considering that such introgressed trees could potentially enhance the adaptability towards prevailing ecological stress (Kormutak et al 2013; Stejskal et al 2016), it is cautious to prioritize their conservation as part of the Sicilian fir recovery program (Jackiw et al 2015; VonHoldt et al 2022; Brauer et al 2023).…”