Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis)

Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.

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.

Born to Be Wild: Evaluating the Zoo-Based Regent Honeyeater Breed for Release Program to Optimise Individual Success and Conservation Outcomes in the Wild

Evaluating the effectiveness of captive breeding programs is central to improving conservation outcomes in released animals. However, few studies have assessed the impact of the strategies and trade-offs involved in husbandry decisions and the selection of traits on the success of breeding programs. This study evaluated a range of husbandry features including an animal's environment, health, and traits of the released individual and its parents involved in the zoo-based Regent Honeyeater breed for release program to optimise individual reproductive success and survivability, leading to improved conservation outcomes in the wild. We analysed 285 birds using a penalised Cox proportional hazard model to assess survival and an ordinal logistic model to evaluate the reproductive success of zoo bred birds released to the wild. Key features identified by the study highlight the importance of having parents that are successful breeders and parents that have an overall higher lifetime reproductive output. However, there were associated quantity-quality trade-offs, as the success of young (i.e., released birds) produced by parents was negatively associated to the number of clutches per year (where one clutch per year was found optimal). The study demonstrated the importance of considering the parental effects on the traits of its offspring beyond its pedigree information and found there was an associated decline in fitness of its offspring with older fathers. Song tutoring using wild Regent Honeyeaters was also important for increased survival post-release. Other important factors are discussed within the review. In general, the study recommended that a multi-faceted approach in the assessment and evaluation of the captive breeding program, to identify markers that will improve conservation outcomes of future releases.

On the use of genome-wide data to model and date the time of anthropogenic hybridisation: an example from the Scottish wildcat

While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of the Scottish wildcat, the UK’s sole extant native felid, with the domestic cat is a good example in this regard. We develop a modelling framework to determine the timescale and mode of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6,546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland, though these individuals are found almost exclusively within the captive breeding program. Most wild-living cats sampled were introgressed to some extent. Additionally, we evaluate the effectiveness of current methods that are used to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.

De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope

Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.

Mummified baboons reveal the far reach of early Egyptian mariners

The Red Sea was witness to important events during human history, including the first long steps in a trade network (the spice route) that would drive maritime technology and shape geopolitical fortunes for thousands of years. Punt was a pivotal early node in the rise of this enterprise, serving as an important emporium for luxury goods, including sacred baboons (Papio hamadryas), but its location is disputed. Here, we use geospatial variation in the oxygen and strontium isotope ratios of 155 baboons from 77 locations to estimate the geoprovenance of mummified baboons recovered from ancient Egyptian temples and tombs. Five Ptolemaic specimens of P. anubis (404–40 BC) showed evidence of long-term residency in Egypt prior to mummification, consistent with a captive breeding program. Two New Kingdom specimens of P. hamadryas were sourced to a region that encompasses much of present-day Ethiopia, Eritrea, and Djibouti, and portions of Somalia and Yemen. This result is a testament to the tremendous reach of Egyptian seafaring during the 2nd millennium BC. It also corroborates the balance of scholarly conjecture on the location of Punt.

First Captive Breeding Program for the Endangered Pyrenean Sculpin (Cottus hispaniolensis Bacescu-Master, 1964)

The strong decline of freshwater fish species in Europe implies that further ex-situ conservation plans should be implemented in the near future. The present study reflects our experience with the Pyrenean sculpin (Cottus hispaniolensis Bacescu-Mester, 1964)—a small cottid endemic to the Hispano-French Garona River basin. In recent years, the Spanish Pyrenean sculpin population has reached a limit situation. Because of that, the non-profit association ADEFFA—with support from the public administration—started the first captive breeding program for this species in 2006. Fourteen years later, this study presents the results and evaluates the different steps of the program, with the aim of discussing and improving the ex-situ conservation plans for this and other cold freshwater species. There is a description and a comparison between six consecutive phases during the captive breeding process: nesting behaviour, courtship, egg fixation, parental care (incubation), hatching and survival during juvenile development. The purposes of this project are to: (1) identify the most determining phases for a successful captive breeding; (2) identify the factors that had a major influence to the success of the critical phases; and (3) increase the number of the offspring. This study is based on thirty-three wild individuals collected from Garona River (Val d’Aran, Spanish Pyrenees). During the program, twelve couples spawned in captive conditions, with around 2300 eggs laid. Eight couples bred successfully, with 751 hatched individuals and 608 juveniles reared. The analysis of each step of the captive breeding does not reveal significant differences between phases, so it can be concluded that they are all critical at the same level. In the literature, similar study-cases of captive breeding programs identify incubation and survival phases as the most critical. Consequently, the management made for this project has probably allowed to overcome in part the main impediments described in other similar programs.

Insights into the successful breeding of Hawksbill sea turtles (Eretmochelys imbricata) from a long-term captive breeding program

Sea turtle populations are declining and evidence-based methods for supporting their populations are required. Captive breeding and release programs can be effective, offering the opportunity to supplement nature populations; however, sea turtles require specific conditions to successfully breed. Here, we present insights gained from a 16 year Hawksbill sea turtle (Eretmochelys imbricata) captive breeding program that was conducted at the Underwater Observatory Marine Park, Eilat, Israel, between 1982-1997. As the first program of its kind for the Hawksbill sea turtle, insights were gained largely through trial-and-error and word of mouth advice. The key insight gained during this program was the critical importance of pre-breeding separation of the sexes; turtles did not breed prior to pre-breeding separation being implemented, but it became predictably regular once it was. Over the course of the program, 161 two-three years old hatchlings were introduced to the Red Sea, which was enabled largely as a result of pre-breeding separation being implemented.

Metabolomic profiling of crayfish haemolymph distinguishes sister species and sex: implications for conservation, aquaculture and physiological studies

Hairy marron (Cherax tenuimanus Smith) are critically endangered freshwater crayfish found only in a single river in south-west Australia. Conservation efforts have included a captive breeding program, which has been largely unsuccessful, despite the closely related smooth marron (Cherax cainii Austin) being successfully bred for aquaculture. Using an untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic approach we created a profile of the metabolites in the haemolymph for males and females of the two species of marron. A non-lethal method was used to collect haemolymph and 84 reproducible annotated metabolites were identified. Variation in the levels of some metabolites were detected between species and between sexes within species. Multivariate analyses clearly differentiated the congeneric species and univariate analyses identified differences between species, sex and for some metabolite interactions between species and sex. This study created a baseline metabolome dataset for the two species and began to investigate the biological significance of metabolites that varied between species. We have shown metabolomics could be used for targeted studies to potentially assist reproductive success. This approach will be beneficial for conservation and aquaculture practices with potential applications for other aquatic taxa worldwide.