No "doom" in chicken domestication?

The wild ancestors of domestic animals as a neglected and threatened component of biodiversity

Domestic animals have immense economic, cultural, and practical value and have played pivotal roles in the development of human civilization. Many domesticates have, among their wild relatives, undomesticated forms representative of their ancestors. Resurgent interest in these ancestral forms has highlighted the unclear genetic status of many, and some are threatened with extinction by hybridization with domestic conspecifics. We considered the contemporary status of these ancestral forms relative to their scientific, practical, and ecological importance; the varied impacts of wild-domestic hybridization; and the challenges and potential resolutions involved in conservation efforts. Identifying and conserving ancestral forms, particularly with respect to disentangling patterns of gene flow from domesticates, is complex because of the lack of available genomic and phenotypic baselines. Comparative behavioral, ecological, and genetic studies of ancestral-type, feral, and domestic animals should be prioritized to establish the contemporary status of the former. Such baseline information will be fundamental in ensuring successful conservation efforts.

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Large-scale genomic analysis reveals the genetic cost of chicken domestication

BACKGROUND

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

RESULTS

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

CONCLUSION

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

The Effects of Domestication on the Brain and Behavior of the Chicken in the Light of Evolution

The avian class is characterized by particularly strong variability in their domesticated species. With more than 250 breeds and highly efficient commercial lines, domestic chickens represent the outcome of a really long period of artificial selection. One characteristic of domestication is the alterations in brain size and brain composition. The influence of domestication on brain morphology has been reviewed in the past, but mostly with a focus on mammals. Studies on avian species have seldom been taken into account. In this review, we would like to give an overview about the changes and variations in (brain) morphology and behavior in the domestic chicken, taking into consideration the constraints of evolutionary theory and the sense or nonsense of excessive artificial selection.

M. Groenen M, Madsen O. Genetic consequences of long-term small effective population size in the critically endangered pygmy hog

Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far-reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole-genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long-term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here, we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations or species). To obtain a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually curated database compiling published data about the genes responsible for evolutionary and domesticated changes across eukaryotes, and examined the >1200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often owing to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared with intraspecific (27%) and interspecific evolution (11%). Although this trend may be subject to detection, publication and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing.