Inbreeding causes decreased seminal quality affecting pregnancy and litter size in the endangered black‐footed ferret

Semen proteome and transcriptome of the endangered black-footed ferret (Mustela nigripes) show association with the environment and fertility outcome

The ex situ population of the endangered black-footed ferret (Mustela nigripes) has been experiencing declines in reproductive success over the past 30 years of human-managed care. A potential cause may be environmental-dependent inbreeding depression with diet being one of the contributing factors since ferrets are not fed their natural diet of prairie dogs. Here, we generated and analyzed semen proteome and transcriptome data from both wild and ex situ ferrets maintained on various diets. We identified 1757 proteins across all samples, with 149 proteins unique to the semen of wild ferrets and forming a ribosomal predicted protein-protein interaction cluster. Wild ferrets also differed from ex situ ferrets in their transcriptomic profile, showing enrichment in ribosomal RNA processing and potassium ion transport. Successful fertility outcomes documented for ex situ ferrets showed the strongest association with the semen transcriptome, with enrichment in genes involved in translation initiation and focal adhesion. Fertility also synergized with the effect of diet on differentially expressed transcriptomes, mainly affecting genes enriched in mitochondrial function. Our data and functional networks are important for understanding the causes and mechanisms of declining fertility in the ex situ ferret population and can be used as a resource for future conservation efforts.

Juvenile ocular abnormalities in a litter of black-footed ferrets

OBJECTIVE

To describe the clinical and histopathological features of ocular abnormalities noted in a litter of black-footed ferrets (Mustela nigripes), including corneal opacification, cataracts, persistent pupillary membranes, microphthalmia, symblepharon and anterior segment malformation.

ANIMALS STUDIED

A litter of eight black-footed ferrets examined at 10 weeks old with a history of ophthalmia neonatorum first noted at 7 days old and histopathological examination of three globes from three ferrets of the same litter between 5 and 7 months old following routine subconjunctival enucleation.

PROCEDURES

Due to the fractious nature of black-footed ferrets, slit-lamp biomicroscopic examination was performed under general isoflurane anesthesia at 10 weeks of age. Corneal opacification was noted in 9/16 eyes, cataracts in 4/16 eyes, and persistent pupillary membranes in 3/16 eyes, among other findings. Histopathology revealed persistent pupillary membranes and Descemet's membrane abnormalities consistent with congenital anterior segment malformation in all three globes. In one ferret, a posterior cortical cataract with posterior lenticular malformation and lens capsule discontinuity was noted. Purulent discharge was cultured at time of enucleation in one ferret with growth of E. coli.

CONCLUSIONS

A novel constellation of ocular malformations with primary congenital and secondary to ophthalmia neonatorum etiologies is described in black-footed ferrets. Due to endangered status of black-footed ferrets, small genetic pool and the requirement for adequate vision for wild-release, congenital ocular abnormalities such as anterior segment malformation and likely the cataracts described are of particular concern. Further investigation and monitoring are warranted to determine the heritability of these ocular abnormalities.

Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes)

Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.

Epigenetic changes to gene pathways linked to male fertility in ex situ black-footed ferrets

Environmental variation can influence the reproductive success of species managed under human care and in the wild, yet the mechanisms underlying this phenomenon remain largely mysterious. Molecular mechanisms such as epigenetic modifiers are important in mediating the timing and progression of reproduction in humans and model organisms, but few studies have linked epigenetic variation to reproductive fitness in wildlife. Here, we investigated epigenetic variation in black-footed ferrets (Mustela nigripes), an endangered North American mammal reliant on ex situ management for survival and persistence in the wild. Despite similar levels of genetic diversity in human-managed and wild-born populations, individuals in ex situ facilities exhibit reproductive problems, such as poor sperm quality. Differences across these settings suggest that an environmentally driven decline in reproductive capacity may be occurring in this species. We examined the role of DNA methylation, one well-studied epigenetic modifier, in this emergent condition. We leveraged blood, testes, and semen samples from male black-footed ferrets bred in ex situ facilities and found tissue-type specificity in DNA methylation across the genome, although 1360 Gene Ontology terms associated with male average litter size shared functions across tissues. We then constructed gene networks of differentially methylated genomic sites associated with three different reproductive phenotypes to explore the putative biological impact of variation in DNA methylation. Sperm gene networks associated with average litter size and sperm count were functionally enriched for candidate genes involved in reproduction, development, and its regulation through transcriptional repression. We propose that DNA methylation plays an important role in regulating these reproductive phenotypes, thereby impacting the fertility of male ex situ individuals. Our results provide information into how DNA methylation may function in the alteration of reproductive pathways and phenotypes in artificial environments. These findings provide early insights to conservation hurdles faced in the protection of this rare species.

Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.

How was genetic diversity transferred with translocations from ex situ to in situ? A case study of the European mink translocation to Hiiumaa Island in Estonia

The European mink (Mustela lutreola) is one of the most threatened small carnivores, listed as Critically Endangered on the IUCN Red List. Tallinn Zoo started a conservation breeding operation in 1980, which in 1992 was shaped into the European mink EEP Program to maintain a demographically and genetically healthy population in captivity. Since 2000, mink have been translocated on a yearly basis from the breeding facility in the zoo to Hiiumaa Island (Estonia) until the formation of the wild island population in 2016. Maintaining a healthy genetic structure in a captive population was a priority, so genetically the least valuable animals, according to calculations made by a population management program, were used for translocation. This study aims to assess the amount of genetic diversity passed from an ex situ population on to the island population. Comparisons of the genetic diversity were made by mitochondrial, microsatellite and nuclear markers. In addition, our results were combined with the pedigree data from the European mink EEP Studbook to further evaluate the flow of genetic diversity from the founder population to the established wild population. According to the findings, the island population's allelic richness was comparable to that of the founder population, and no evidence was found that its genetic structure had diverged from that of the founder population. It seems that the formation of the island population has been a gradual process of no more than the last seven yearly translocations.

The Cranial Morphology of the Black-Footed Ferret: A Comparison of Wild and Captive Specimens

The black-footed ferret (Mustela nigripes), a North American mustelid species, was once found abundantly throughout the Midwest until the extreme decline in prairie dogs (Cynomys spp.), the black-footed ferret's primary food source, brought the species to near-extinction. Subsequently, the Black-Footed Ferret Recovery Program was created in the 1980s with a goal of bringing all remaining individuals of the species into captivity in order to breed the species back to a sustainable population level for successful reintroduction into the wild. While many components of the ferrets' health were accounted for while in captivity-especially those affecting fecundity-this study aims to assess the effects that captivity may have had on their cranial morphology, something that has not been widely studied in the species. In a previous study, we showed that the captive ferrets had significant oral health problems, and here we aim to document how the captive diet also affected their skull shape. For this study, 23 cranial measurements were taken on the skulls of 271 adult black-footed ferrets and 53 specimens of two closely related species. Skulls were divided based on sex, species, captivity status and phase of captivity and compared for all measurements using stepwise discriminant analysis as well as principal component analysis derived from the combined variables. We found that there are significant differences between captive and wild specimens, some of which are larger than interspecific variation, and that a diet change in the captive specimens likely helped decrease some of these differences. The results suggest that captivity can cause unnatural cranial development and that diet likely has a major impact on cranial morphology.

Strategies for establishing and using genome resource banks to protect genetic diversity in conservation breeding programs

Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but there are few guidelines for integrating GRBs into established breeding programs. Here we present basic guidelines, focusing on strategies for the collection, maintenance, and use of semen GRBs for protecting genetic diversity. These guidelines should be applied in the context of the specific purposes and roles of a breeding program's GRB, which will differ among species depending on vulnerability to loss and the status of rescue and conservation efforts. We recommend establishing up to three types of collections: (1) a National Reserve to preserve a species' genetic diversity, to be used only as a last resort; (2) a Savings Account to be used periodically to invigorate a genetically depauperate population; and (3) a Checking Account to be used as a regular part of the breeding program. We present methods for identifying donors to maximize genetic diversity in a GRB, as well as strategies for maintaining and optimally using GRBs.

Population genetic structure of the Natterjack toad (Epidalea calamita) in Ireland: implications for conservation management

Molecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Sperm morphometry is affected by increased inbreeding in the Retinta cattle breed: A molecular approach

The effect of inbreeding depression on sperm motility is well documented, but its influence on sperm morphometry has been scarcely examined to date. Here, we combined the use of computer-assisted sperm morphometry analysis (CASMA) with a SNP-based genomic approach to determine and characterize the effect of inbreeding on the sperm shape of a highly inbred cattle population. We determined seven morphometric parameters on frozen-thawed sperm samples of 57 Retinta bulls: length (L, µm), width (W, µm), area (A, µm² ), perimeter (P, µm), ellipticity (ELI; L/W), elongation (L-W)/(L + W) and perimeter-to-area shape factor (p2a; P² /4 × π × A). The comparison of highly inbred (HI) and lowly inbreed (LI) individuals based on runs of homozygosity (ROH) inbreeding values (F _ROH ) showed no differences between groups. An additional two-step unsupervised sperm subpopulation analysis based on morphometric parameters showed significant differences in the abundance of different sperm subpopulations between groups (p < 0.05). This analysis revealed that HI bulls harbored a higher percentage of narrow-head sperm as opposed to the higher percentage of large- and round-headed sperm detected in LI. A further genomic characterization revealed 23 regions differentially affected by inbreeding in both groups, detecting six genes (SPAG6, ARMC3, PARK7, VAMP3, DYNLRB2, and PHF7) previously related to different spermatogenesis-associated processes.

Using hair cortisol analysis to understand the biological factors that affect black-footed ferret (Mustela nigripes) stress physiology

The black-footed ferret (Mustela nigripes) was driven to near extinction due to habitat loss and an introduced disease, sylvatic plague (Yersinia pestis). After 35 years of breeding in ex situ facilities, the black-footed ferret has been experiencing infertility with seminal traits declining in males and only about a third of breeding-aged females are whelping. Our goal was to use hair cortisol analysis to determine if the ex situ population was experiencing chronic stress that was affecting reproduction by comparing captive ferrets to wild individuals. Our specific objectives were to (i) compare hair cortisol concentrations (HCCs) between age classes (juveniles versus adults), (ii) compare the HCCs of in situ and across different ex situ facilities and (iii) determine the relationship between HCCs and reproductive success. Overall, wild juveniles had higher HCC than wild adults. Our generalized linear mixed model determined that the parameters that best predict HCC for adults were the interactions among sex, in situ versus ex situ facilities and season. During both seasons, wild females had higher HCCs compared to the ex situ females. During the breeding season, male HCCs across breeding facilities varied and males at the breeding facility with the largest ferret habitats had HCCs similar to wild males. At one breeding facility, HCC was higher in males that sired compared to those that did not sire. In conclusion, ex situ ferrets do not have higher HCC than wild individuals when controlling for season and ex situ habitat size, and ex situ males with higher HCC tended to sire. This suggests that HCC may be metabolically driven and/or that low HCC may be an indication of hypothalamus-pituitary-adrenal axis dysregulation and warrants further investigation both for laboratory validation and biological relevance.

Influence of vitamin E and carcass feeding supplementation on fecal glucocorticoid and androgen metabolites in male black-footed ferrets (Mustela nigripes)

In recent years, the ex situ population of the endangered black-footed ferret (Mustela nigripes; ferret) has experienced a decline in normal sperm morphology (from 50% to 20%), which may be linked to inbreeding depression and/or a dietary change. We examined the effects of adding carcass and vitamin E to the diet on stress and reproductive biomarkers in male ferrets (n = 42 males including 16 juveniles and 26 adults) housed at the U.S. Fish and Wildlife National Black-footed Ferret Conservation Center (Carr, CO, USA). Fecal samples (3x/week) were collected from November and December (pre-breeding season, no diet change), February through May (breeding season, diet change) and June (post-breeding season, diet change) and analyzed for fecal glucocorticoid metabolites (FGM) via a corticosterone enzyme immunoassay (EIA). A subset of samples from adult males (n = 15) were analyzed for fecal androgen metabolites (FAM) via a testosterone EIA. We first used a linear mixed effects model to identify the important fixed effects among meat treatment, vitamin E treatment, age class (juvenile or adult), and all possible interactions on each hormone. We then examined the important factor’s effects across seasons using the non-parametric Friedman test. We found that age did not influence (p = 0.33) FGMs; however there was a significant effect of meat treatment on FGM (p = 0.04) and an effect of vitamin E on FAMs (p<0.10). When fed carcass, FGMs declined (p<0.001) from pre- to the during the breeding season time period, but was similar (p>0.05) between during and post-breeding season periods. Males that were not fed carcass had higher (p<0.05) FGMs during the breeding season compared to pre- and post-breeding season and FGMs were lower (p<0.05) in the post-breeding season compared to pre-breeding season. Males fed with carcass had lower (p<0.001) FGM than males that were not fed carcass during both the pre-breeding and the breeding season but not during the post-breeding season (p>0.05). Males supplemented with vitamin E had higher (p<0.001) FAM than non-supplemented males during the breeding season only. For both groups, FAM was highest (p<0.05) during the breeding season. In conclusion, adding carcass to the diet can reduce glucocorticoid production and adding vitamin E can increase testosterone during the breeding season, which may influence reproductive success.

Cryopreservation of ferret (Mustela putorius furo) sperm collected by rectal massage and electroejaculation: Comparison of a decelerating and an accelerating freezing rate protocol

The domestic ferret (Mustela putorius furo) provides a good model for developing new reproductive technologies for use with threatened related species. Such technologies could also be used in the reproductive management of this pet species. The present work reports an improved freezing protocol for ferret sperm. Semen was collected by electroejaculation plus rectal massage (in an attempt to reduce the electrical stimulation necessary) from five adult male ferrets, and then subjected to one of two freezing protocols: (a) from 5 to −35°C at 40°C/min, then from −35 to −65°C at 17°C/min, and finally from −65 to −85°C at 3°C/min—a decelerating freezing rate; and (b) from 5 to − 10°C at 5°C/min, and then from −10 to −130°C at 60°C/min—an accelerating freezing rate. After thawing, the viability and acrosomal integrity of the sperm frozen via the two‐step accelerating method were better than those frozen via the three‐step decelerating method (43.3 ± 3.5% and 71.2 ± 3.4% compared with 29.7 ± 3.7% and 58.8 ± 3.4% respectively; p < .05). No differences were seen between the methods with respect to sperm motility variables; most sperm (>90%) remained static with both freezing methods. In conclusion, although the method with accelerating freezing rate was associated with better post‐thaw sperm viability and acrosome integrity values, neither of the two freezing methods tested provided adequate motility results after thawing. Combining rectal massage with electrical stimuli seemed to reduce the number of the latter required for successful sperm collection.

Urethral catheterization as an alternative method for collecting sperm in the black-footed ferret (Mustela nigripes)

The endangered black-footed ferret (BFF; Mustela nigripes) is an important example of the benefits of assisted reproduction in species conservation with both semen evaluation and artificial insemination using fresh and frozen sperm being successfully incorporated into the breeding program. Currently, electroejaculation (EE) is routinely utilized for semen collection in BFFs, a technique that requires custom equipment and experienced operators, and does not consistently yield viable samples in this species. In this case study, we evaluated the feasibility of urethral catheterization (UC) for semen collection, a method predominately tested in domestic and non-domestic felids, on four occasions (three BFF males). After general anesthesia with a combination of ketamine, midazolam and α2-agonist dexmedetomidine (thought to promote semen release into the urethra), a lightly lubricated, flexible feeding tube was passed into the urethral opening and advanced ~7-8 cm into the urethra. A syringe attached to the feeding tube was used to apply mild negative pressure to collect sperm. Semen samples were successfully collected on all four attempts. Sperm characteristics ranged as follows: 10.5-26.0 × 10⁶ sperm/ml concentration, 50-90% motility and 36-61% normal sperm morphology. This is the first report of the use of UC as a potential alternative to EE in the BFF, a more field-friendly technique that is less invasive and more consistent for obtaining samples free of urine contamination.

Genetic signature of disease epizootic and reintroduction history in an endangered carnivore

Emerging infectious diseases have recently increased in wildlife and can result in population declines and the loss of genetic diversity in susceptible populations. As populations of impacted species decline, genetic diversity can be lost, with ramifications including reduced effective population size and increased population structuring. For species of conservation concern, which may already have low genetic diversity, the loss of genetic diversity can be especially important. To investigate the impacts of a novel pathogen on genetic diversity in a genetically depauperate endangered species, we assessed the ramifications of a sylvatic plague-induced bottleneck in black-footed ferrets (Mustela nigripes). Following a plague epizootic, we genotyped 184 ferrets from Conata Basin and Badlands National Park, South Dakota, at seven microsatellite loci. We compared our results to pre-plague studies in the same population. We observed population substructuring into three genetic clusters. These clusters reflect founder effects from ferret reintroduction events followed by genetic drift. Compared to the pre-plague population, we observed losses of allelic diversity in all clusters, as well as significantly reduced heterozygosity in one cluster. These results indicate that disease epizootics may reduce population size and also genetic diversity. Our results suggest the importance of early and sustained management in mitigating disease epizootics in naïve populations for the maintenance of genetic diversity.

Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations

Human-induced changes to environments are causing species declines. Beyond preserving habitat (in situ), insurance (ex situ) populations are essential to prevent species extinctions. The Conservation Centers for Species Survival (C2S2) is leveraging space of breeding centers and private ranches to produce “source populations”—genetically diverse reservoirs that also support research and reintroductions. The initial focus is on four African antelopes. C2S2 has developed a program, the Source Population Alliance, that emphasizes animals living in spacious, naturalistic conditions in greater numbers than can be accommodated by urban zoos. Simulation modeling demonstrates how herds can rapidly increase population abundance and retain genetic diversity. Advances in genomics and resulting DNA data allow monitoring of genetic diversity and parentage as well as refined decision-making. This approach, neither pure in situ nor ex situ, but rather “sorta situ”, is an innovative way of linking public and private sector resources to ensure that endangered species survive.