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.

Long-term Preservation of Testicular Tissue Integrity and Viability Using Vitrification in the Endangered Black-Footed Ferret (Mustela Nigripes)

Simple Summary

In addition to semen preservation, systematic cryo-banking of testicular tissues is critical to preserve the genetic value of recently deceased or neutered black-footed ferrets. Mature sperm cells produced from vitrified-warmed tissues could be used for in vitro fertilization over multiple generations, which would enhance the genetic management of this rare and endangered species. The objective of the study was to evaluate structural and functional properties of vitrified testicular tissues directly after warming or after warming plus a short period of in vitro culture. Fresh, vitrified/warmed, and warmed/cultured tissues from five adults were analyzed through histology, DNA fragmentation, cell survival, and germ cell composition. Percentages of intact seminiferous tubules decreased right after vitrification/warming and improved after culture (reaching same percentages as the fresh controls). While proportions of cells with intact DNA and viable cells were affected by vitrification/warming, they were then similar or better after additional culture than in the fresh tissue. Proportions of cells labeled with differentiation markers also increased during in vitro culture. We demonstrated for the first time that black-footed ferret testicular tissues can be vitrified and revived, which will potentially contribute to new strategies to enhance assisted reproduction as well as conservation efforts in that rare and endangered species.

Abstract

Systematic cryo-banking of semen and testicular tissues is critical to preserve the genetic value of recently deceased or neutered black-footed ferrets (BFFs). Specifically, recovering or producing mature sperm cells from vitrified-warmed issues offers additional options in assisted reproduction. This could, in turn, enhance the genetic management of this rare and endangered species over multiple generations. The objective of the study was to evaluate structural properties, DNA fragmentation, cell viability, and germ cell composition in vitrified testicular tissues from BFFs directly after warming or after warming plus a short in vitro culture period. Tissue biopsies from five adult BFFs were either kept fresh or vitrified with a standard protocol (using dimethylsulphoxide (DMSO) and glycerol) and warmed at 50 °C for 5 s. Some of the warmed samples were then cultured in vitro for 24 h. Fresh, warmed, and warmed/cultured tissues were analyzed using different indicators: histology of seminiferous tubules, intact Sertoli cells (vimentin labeling), DNA integrity, cell viability, germ cell composition (Oct4 and Boule labeling). Percentages of intact seminiferous tubules decreased after vitrification/warming and returned to the level of fresh samples after culture. While percentages of cells labeled with vimentin, with intact DNA integrity, or proportions of viable cells were affected by vitrification/warming, they all reached similar or better levels than the fresh tissue after culture. Proportions of cells labeled with Boule antibodies also improved during in vitro culture post-warming. We demonstrated for the first time that BFF testes subjected to vitrification, rapid warming, and short in vitro culture were viable and maintained the ability to resume germ cell progression. Cryopreserved testicular tissues could potentially contribute to new strategies to enhance BFF assisted reproduction as well as conservation efforts.

Climate change impacts on the conservation outlook of populations on the poleward periphery of species ranges: A case study of Canadian black-tailed prairie dogs (Cynomys ludovicianus)

Given climate change, species' climatically suitable habitats are increasingly expected to shift poleward. Some imperilled populations towards the poleward edge of their species' range might therefore conceivably benefit from climate change. Interactions between climate and population dynamics may be complex, however, with climate exerting effects both indirectly via influence over food availability and more directly, via effects on physiology and its implications for survival and reproduction. A thorough understanding of these interactions is critical for effective conservation management. We therefore examine the relationship between climate, survival and reproduction in Canadian black-tailed prairie dogs, a threatened keystone species in an imperilled ecosystem at the northern edge of the species' range. Our analyses considered 8 years of annual mark-recapture data (2007-2014) in relation to growing degree days, precipitation, drought status and winter severity, as well as year, sex, age and body mass. Survival was strongly influenced by the interaction of drought and body mass class, and winter temperature severity. Female reproductive status was associated with the interaction of growing degree days and growing season precipitation, with spring precipitation and with winter temperature severity. Results related to body mass suggested that climatic variables exerted their effects via regulation of food availability with potential linked effects of food quality, immunological and behavioural implications, and predation risk. Predictions of future increases in drought conditions in North America's grassland ecosystems have raised concerns for the outlook of Canadian black-tailed prairie dogs. Insights gained from the analyses, however, point to mitigating species management options targeted at decoupling the mechanisms by which climate exerts its negative influence. Our approach highlights the importance of understanding the interaction between climate and population dynamics in peripheral populations whose viability might ultimately determine their species' ability to track climatically suitable space.

Vaccines for Conservation: Plague, Prairie Dogs & Black-Footed Ferrets as a Case Study

The endangered black-footed ferret (Mustela nigripes) is affected by plague, caused by Yersinia pestis, both directly, as a cause of mortality, and indirectly, because of the impacts of plague on its prairie dog (Cynomys spp.) prey base. Recent developments in vaccines and vaccine delivery have raised the possibility of plague control in prairie dog populations, thereby protecting ferret populations. A large-scale experimental investigation across the western US shows that sylvatic plague vaccine delivered in oral baits can increase prairie dog survival. In northern Colorado, an examination of the efficacy of insecticides to control fleas and plague vaccine shows that timing and method of plague control is important, with different implications for long-term and large-scale management of Y. pestis delivery. In both cases, the studies show that ambitious field-work and cross-sectoral collaboration can provide potential solutions to difficult issues of wildlife management, conservation and disease ecology.