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

The last red wolves were captured along the Gulf Coast in 1980, where they hybridized with coyote, to establish the captive breeding population. However, red wolf ancestry persists in local coyotes and could be leveraged by genomic innovations to support species persistence. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana, and find they carried 38-62% red wolf ancestry acquired in the last 30 years, which is enriched on land with minimal coyote hunting. These coyotes were also similar in ancestry to canids captured in the 1970s that initiated the red wolf captive breeding program. Further, we reported that coyotes with higher red wolf ancestry are larger in size. Our findings evidence the importance of hybrids as a reservoir of endangered species ancestry for contemporary conservation efforts. Admixed genomes are at the forefront of innovative solutions, with red wolf survival a prime candidate for this new paradigm.

Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast

Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographic and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all the while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 102,621 SNP loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along an east-to-west gradient across the southern United States that was associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographic zone where the last red wolves were known prior to their extinction in the wild, contained the highest and oldest levels of red wolf ancestry. X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, suggestive of the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographic and genomic extent of cryptic red wolf ancestry can provide novel and variable genomic resources for the survival of the endangered red wolf.

Wild red wolf Canis rufus poaching risk

The reintroduced red wolf population in northeastern North Carolina declined to 7 known wolves by October 2020. Poaching (illegal killing) is the major component of verified anthropogenic mortality in this and many other carnivore populations, but it is still not well understood. Poaching is often underestimated, partly as a result of cryptic poaching, when poachers conceal evidence. Cryptic poaching inhibits our understanding of the causes and consequences of anthropogenic mortality which is important to conservation as it can inform us about future population patterns within changing political and human landscapes. We estimate risk for marked adult red wolves of 5 causes of death (COD: legal, nonhuman, unknown, vehicle and poached) and disappearance, describe variation in COD in relation to hunting season, and compare time to disappearance or death. We include unknown fates in our risk estimates. We found that anthropogenic COD accounted for 0.724 – 0.787, including cryptic and reported poaching estimated at 0.510 – 0.635 of 508 marked animals. Risk of poaching and disappearance was significantly higher during hunting season. Mean time from collaring until nonhuman COD averaged 376 days longer than time until reported poached and 642 days longer than time until disappearance. Our estimates of risk differed from prior published estimates, as expected by accounting for unknown fates explicitly. We quantify the effects on risk for three scenarios for disappearances, which span conservative to most likely COD. Implementing proven practices that prevent poaching or hasten successful reintroduction may reverse the decline to extinction in the wild of this critically endangered population. Our findings add to a growing literature on endangered species protections and enhancing the science used to measure poaching worldwide.

Multiple FGF4 Retrocopies Recently Derived within Canids

Two transcribed retrocopies of the fibroblast growth factor 4 (FGF4) gene have previously been described in the domestic dog. An FGF4 retrocopy on chr18 is associated with disproportionate dwarfism, while an FGF4 retrocopy on chr12 is associated with both disproportionate dwarfism and intervertebral disc disease (IVDD). In this study, whole-genome sequencing data were queried to identify other FGF4 retrocopies that could be contributing to phenotypic diversity in canids. Additionally, dogs with surgically confirmed IVDD were assayed for novel FGF4 retrocopies. Five additional and distinct FGF4 retrocopies were identified in canids including a copy unique to red wolves (Canis rufus). The FGF4 retrocopies identified in domestic dogs were identical to domestic dog FGF4 haplotypes, which are distinct from modern wolf FGF4 haplotypes, indicating that these retrotransposition events likely occurred after domestication. The identification of multiple, full length FGF4 retrocopies with open reading frames in canids indicates that gene retrotransposition events occur much more frequently than previously thought and provide a mechanism for continued genetic and phenotypic diversity in canids.

Experience of using clove oil for olfactory enrichment in Russian Zoos

Successful experiments on olfactory enrichment of clove oil in Russian zoos have been carried out. Olfactory enrichment with clove oil reduced or eliminated stereotypical behavior (pacing) in most Amur tigers, African lions, and some Canadian and Red wolves. The behavior of the Far Eastern leopard and the Snow leopard behavior has not changed significantly under the influence of clove essential oil. Olfactory enrichment of clove essential oil is more successful for young animals.

Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7000 single nucleotide polymorphisms (SNPs) in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.

Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the Gulf Coast region since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7,000 SNPs in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.