Genomic recovery lags behind demographic recovery in bottlenecked populations of the Channel Island fox, Urocyon littoralis

Abstract

With continued global change, recovery of species listed under the Endangered Species Act is increasingly challenging. One rare success was the recovery and delisting of the Channel Island fox (Urocyon littoralis) after 90%-99% population declines in the 1990s. While their demographic recovery was marked, less is known about their genetic recovery. To address genetic changes, we conducted the first multi-individual and population-level direct genetic comparison of samples collected before and after the recent bottlenecks. Using whole-exome sequencing, we found that already genetically depauperate populations were further degraded by the 1990s declines and remain low, particularly on San Miguel and Santa Rosa Islands, which underwent the most severe bottlenecks. The two other islands that experienced recent bottlenecks (Santa Cruz, and Santa Catalina islands) showed mixed results based on multiple metrics of genetic diversity. Previous island fox genomics studies showed low genetic diversity before the declines and no change after the demographic recovery, thus this is the first study to show a decrease in genetic diversity over time in U. littoralis.Additionally, we found that divergence between populations consistently increased over time, complicating prospects for using inter-island translocation as a conservation tool. The Santa Catalina subspecies is now federally listed as threatened, yet other de-listed subspecies are still recovering genetic variation which may limit their ability to adapt to changing environmental conditions. This study further demonstrates that species conservation is more complex than population size and that some island fox populations are not yet 'out of the woods'.

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

“…Red squirrel populations in Scotland exhibit some of the lowest heterozygosity reported for wild mammals (Fig. 4), and are comparable to species noted for extreme genetic impoverishment such as the Channel Island fox Urocyon littoralis (Adams and Edmands, 2023;Robinson et al, 2016), Iberian lynx Lynx pardinus (Abascal et al, 2016) and cheetah…”

“…Interventions of this type are becoming ever more common as wild populations become increasingly fragmented and disjunct. Founder effects, exacerbated by population fragmentation, have been observed across species (Adams and Edmands, 2023;Colpitts et al, 2022;Kumar et al, 2023;Wilder et al, 2022), and many genetically depauperate species are now successfully managed using a metapopulation strategy. For example, Kenyan populations of the eastern black rhinoceros Diceros bicornus micheali are now wholly managed as a country-wide metapopulation (Amin et al, 2017), and notable success has also been recorded…”

The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine‐scale differentiation across host species and island populations

“…While island foxes are found on six of eight islands in the archipelago, island spotted skunks are only found on the two largest islands. Throughout their range, both species have undergone significant population fluctuations and currently exhibit low levels of genetic diversity, rendering them of particular conservation concern (Adams & Edmands, 2023 ; Floyd et al., 2011 ; Jones et al., 2013 ; Robinson et al., 2016 ). These species are also of interest to population ecologists, as they serve as a rare example of mammalian carnivore coexistence in island habitats.…”