Genomic signatures of domestication in Old World camels

Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, here we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pan-domestication set - and overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication. Robert R. Fitak et al. investigate the genetic basis for domestication in camels. They found that the positive selection of candidate domestication genes is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Their work provides insights to the evolutionary history of camels and genetics of domestication.Peer reviewe

Reconstruction of the major maternal and paternal lineages in the feral New Nealand Kaimanawa horses

New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today’s KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse

Conservation Genomics of the Endangered Mexican Wolf and De Novo SNP Marker Development in Pumas using Next-Generation Sequencing

Traditionally, conservation genetics has examined neutral-marker (e.g microsatellite) surveys to inform the conservation and management of species. The field expanded together with the expansion of molecular biology, primarily enabled by polymerase chain reaction (PCR) and DNA sequencing technologies. Recently, advances in genomics and bioinformatics, notably next-generation sequencing (NGS), have demonstrated the ability to further enhance conservation genetic assessments. As a result, conservation genetics is rapidly transforming into a field of conservation genomics. Although complete genome sequencing and analysis is still beyond the reach of many conservation genetic projects, researchers can benefit by producing large amounts of genetic data quickly for their species of interest, or by exploiting existing genomic data for a closely related species. The research presented below serves as an example of these two different approaches. First, I review the current state of conservation genomics, utilizing examples when appropriate to illustrate different techniques and approaches. Next, I describe the development of a tool using NGS that is useful for the rapid genetic analysis of pumas (Puma concolor) called PumaPlex. This work details the methods involved and will be useful for anyone interested in working with a species where little genomic data is available. The last three chapters focus on using an existing genomic tool for the domestic dog to analyze admixture, quantify inbreeding, and identify potential adaptive variation in the endangered Mexican wolf (Canis lupus baileyi). The results demonstrated the Mexican wolf has no significant recent ancestry from domestic dogs, and that several loci may potentially be effective in increasing fitness in the reintroduced population