The Effects of Captivity on the Mammalian Gut Microbiome

Recent studies increasingly note the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biology (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and, consequently, the health of hosts. Animals living in captivity experience a range of changes that may influence the gut bacteria, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals. However, these studies are relatively limited in the scope of species that have been examined. Here we present a dataset that includes paired wild and captive samples from mammalian taxa across six Orders to investigate generalizable patterns of the effects captivity on mammalian gut bacteria. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the taxa surveyed, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that demonstrated larger shifts in relative abundance between the captive and wild states included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.

Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse

Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878-1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations.

Alliances and reproductive success in Camargue stallions

A study of a herd of Camargue horses Equus caballus, showed that while the majority of high-ranking stallions held single-male harems, some sons of low-ranking mares, being low ranking themselves, formed alliances that could last a lifetime. The two stallions were each other's closest associate and preferential grooming partner. Alliances were based on coalitions in which either both partners confronted an intruder synchronously or the dominant of the pair tended the female(s) while the subordinate simultaneously displayed towards the rival. Alliance partners were of similar age but were not more closely related to each other than to other stallions in the herd. Long-term paternity data revealed that subordinates sired close to a quarter of the foals born into the alliance group, and significantly more foals than low-ranking stallions in the herd adopting a 'sneak'-mating strategy. The dominant appeared to benefit from the presence of his subordinate partner. Fights occurred all year round, and the subordinate stallion of each alliance pair fought outside competitors more than twice as often as the dominant. Forming short-term alliances before defending mares on their own may enhance long-term reproductive success for both partners. Other benefits to both partners include higher survivorship of their foals and increased access to proven reproductive mares. These results suggest that the relationship between alliance partners is based on mutualism, but several conditions for reciprocity seem to be fulfilled: the benefit to the dominant (assistance in fights), and the benefit to the subordinate (access to reproduction), are both costly to the other partner and delayed in time. Copyright 1999 The Association for the Study of Animal Behaviour.