High genetic load without purging in caribou, a diverse species at risk.

High intra-specific genetic diversity is associated with adaptive potential, which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, thereby increasing the risk of inbreeding depression if population sizes decrease. Purging of deleterious variation has been demonstrated in some threatened species. However, less is known about the costs of declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that are expected to undergo population declines. Caribou is a species of ecological and cultural significance in North America with a wide distribution supporting extensive phenotypic variation but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole-genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We found highly divergent levels of inbreeding across individuals, including the loss of alleles by drift but not increased purging in inbred individuals, which had more homozygous deleterious alleles. We also found comparable frequencies of homozygous deleterious alleles between lineages regardless of nucleotide diversity. Thus, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the "double-edged sword" of genetic diversity that may be representative of other species atrisk affected by anthropogenic activities.

Paranannizziopsis spp. infections in wild snakes and a qPCR assay for detection of the fungus.

The emergence of ophidiomycosis (or snake fungal disease) in snakes has prompted increased awareness of the potential effects of fungal infections on wild reptile populations. Yet, aside from Ophidiomyces ophidiicola, little is known about other mycoses affecting wild reptiles. The closely related genus Paranannizziopsis has been associated with dermatomycosis in snakes and tuataras in captive collections, and P. australasiensis was recently identified as the cause of skin infections in non-native wild panther chameleons (Furcifer pardalis) in Florida, USA. Here we describe five cases of Paranannizziopsis spp. associated with skin lesions in wild snakes in North America and one additional case from a captive snake from Connecticut, USA. In addition to demonstrating that wild Nearctic snakes can serve as a host for these fungi, we also provide evidence that the genus Paranannizziopsis is widespread in wild snakes, with cases being identified in Louisiana (USA), Minnesota (USA), Virginia (USA), and British Columbia (Canada). Phylogenetic analyses conducted on multiple loci of the fungal strains we isolated identified P. australasiensis in Louisiana and Virginia; the remaining strains from Minnesota and British Columbia did not cluster with any of the described species of Paranannizziopsis, although the strains from British Columbia appear to represent a single lineage. Finally, we designed a pan-Paranannizziopsis real-time PCR assay targeting the internal transcribed spacer region 2. This assay successfully detected DNA of all described species of Paranannizziopsis and the two potentially novel taxa isolated in this study and did not cross-react with closely related fungi or other fungi commonly found on the skin of snakes. The assay was 100% sensitive and specific when screening clinical (skin tissue or skin swab) samples, although full determination of the assay's performance will require additional follow up due to the small number of clinical samples (n = 14 from 11 snakes) available for testing in our study. Nonetheless, the PCR assay can provide an important tool in further investigating the prevalence, distribution, and host range of Paranannizziopsis spp. and facilitate more rapid diagnosis of Paranannizziopsis spp. infections that are otherwise difficult to differentiate from other dermatomycoses.

Genomics of founders for conservation breeding: the Jasper caribou case.

Conservation breeding programs are increasingly used as recovery actions for wild animals; bringing founders into captivity to rear captive populations for future reintroduction into the wild. The International Union for the Conservation of Nature recommends that founders should come from genetically close populations and should have sufficient genetic diversity to avoid mating among relatives. Genomic data are highly informative for evaluating founders due to their high resolution and ability to capture adaptive divergence, yet, their application in that context remains limited. Woodland caribou are federally listed as a Species at Risk in Canada, with several populations facing extirpation, such as those in the Rocky Mountains of Alberta and British Columbia (BC). To prevent local extirpation, Jasper National Park (JNP) is proposing a conservation breeding program. We examined single nucleotide polymorphisms for 144 caribou from 11 populations encompassing a 200,0002 km area surrounding JNP to provide information useful for identifying appropriate founders for this program. We found that this area likely hosts a caribou metapopulation historically characterized by high levels of gene flow, which indicates that multiple sources of founders would be appropriate for initiating a breeding program. However, population structure and adaptive divergence analyses indicate that JNP caribou are closest to populations in the BC Columbia range, which also have suitable genetic diversity for conservation breeding. We suggest that collaboration among jurisdictions would be beneficial to implement the program to promote recovery of JNP caribou and possibly other caribou populations in the surrounding area, which is strategically at the periphery of the distribution of this endangered species. Supplementary Information: The online version contains supplementary material available at 10.1007/s10592-023-01540-3.

FASCIOLOIDES MAGNA IN FREE-RANGING ROCKY MOUNTAIN BIGHORN SHEEP (OVIS CANADENSIS).

From February to May 2021, four nonmigratory rams from the Radium-Stoddart bighorn sheep (BHS; Ovis canadensis) herd in the Rocky Mountains of southeastern British Columbia, Canada, died from infection with the giant liver fluke, Fascioloides magna. Affected animals were emaciated, weak, and lethargic or were found dead. Gross lesions, histopathology, and parasite burdens were consistent with those reported in experimentally infected BHS, domestic sheep, and other aberrant hosts. Although BHS range does not typically overlap with fluke-contaminated aquatic habitats, the change in migratory behavior recently observed in some Radium-Stoddart rams may have exposed the affected animals to F. magna. We describe clinical signs and gross and histopathologic findings of hepatobiliary trematodiasis associated with F. magna in free-ranging BHS. From experimental data and our findings, giant liver fluke is pathogenic and is a threat to the conservation of the Radium-Stoddart BHS herd and other BHS herds in endemic F. magna regions.

Corynosoma strumosum (Acanthocephala) infection in marine foraging mink (Neogale vison) and river otter (Lontra canadensis) and associated peritonitis in a juvenile mink.

Corynosoma strumosum (Acanthocephala), a widespread parasite of pinnipeds, is reported in marine foraging North American mink (Neogale vison) and river otter (Lontra canadensis) on Vancouver Island, British Columbia. This is the first confirmed case of infection by C. strumosum in river otters on the west coast of North America and may be the first confirmed case of infection in wild North American mink; C. strumosum has previously been reported in river otters in Europe (Lutra lutra) and in farmed mink fed with marine fish. We also detected a case of acanthocephalan associated peritonitis in a juvenile mink. Furthermore, though infections with Corynosoma spp. are often assumed to be accidental in mustelids, some C. strumosum individuals found in mink showed signs of reproductive activity. These findings indicate that mink may be a competent definitive host and represent a reservoir in coastal habitats although further research is needed to confirm this. Investigating whether river otters may be competent hosts and determine the prevalence of infection in coastal populations would determine the potential implications of C. strumosum for coastal otters and minks. Our report indicates that mink and possibly river otter living in coastal areas are vulnerable to this previously unreported parasitic infection with mortality risk, at least in juvenile individuals.

SARS-CoV-2 wildlife surveillance surrounding mink farms in British Columbia, Canada.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect many wild and domestic animal species. Farmed American mink (Neovison vison) are particularly susceptible to infection. Outbreaks of SARS-CoV-2 were detected in farmed mink on three mink farms in British Columbia (BC), Canada between December 2020 and May 2021. In BC, mink farm density and proximity to wildlife habitats increase transmission risks from infected farmed mink. The objective of this study is to investigate the risk of SARS-CoV-2 spreading to and from wildlife in the area surrounding infected mink farms in BC, Canada, as well as to compare the effectiveness of physical and camera trapping surveillance methodologies. Methods: A combination of physical and camera trapping was used on and around three BC mink farms with active SARS-CoV-2 infections between January 22, 2021, and July 10, 2021. Samples from trapped animals, including escaped farmed mink, were tested for SARS-CoV-2. Camera images from one mink farm were reviewed to determine species and proximity to the mink barn. Results: Seventy-one animals of nine species were captured and sampled. Three captured mink tested positive for SARS-CoV-2 by polymerase chain reaction and serology; the remaining samples were negative for SARS-CoV-2. Genotyping of the three positive mink indicated these were domestic (vs. wild) mink. A total of 440 animals of 16 species were photographed at the one farm where cameras were deployed. Conclusion: Detection of SARS-CoV-2 in escaped farmed mink is concerning and demonstrates the potential for transmission from farmed mink to wildlife, particularly given the observation of wildlife known to be susceptible to SARS-CoV-2 near infected mink farms. Combined use of physical and camera trapping contributed to the breadth of the results and is strongly recommended for future surveillance.