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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

ABSTRACT: The domestication of the horse ? 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.

SUBMITTER: Schubert M

PROVIDER: S-EPMC4284583 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

Schubert Mikkel M Jónsson Hákon H Chang Dan D Der Sarkissian Clio C Ermini Luca L Ginolhac Aurélien A Albrechtsen Anders A Dupanloup Isabelle I Foucal Adrien A Petersen Bent B Fumagalli Matteo M Raghavan Maanasa M Seguin-Orlando Andaine A Korneliussen Thorfinn S TS Velazquez Amhed M V AM Stenderup Jesper J Hoover Cindi A CA Rubin Carl-Johan CJ Alfarhan Ahmed H AH Alquraishi Saleh A SA Al-Rasheid Khaled A S KA MacHugh David E DE Kalbfleisch Ted T MacLeod James N JN Rubin Edward M EM Sicheritz-Ponten Thomas T Andersson Leif L Hofreiter Michael M Marques-Bonet Tomas T Gilbert M Thomas P MT Nielsen Rasmus R Excoffier Laurent L Willerslev Eske E Shapiro Beth B Orlando Ludovic L

Proceedings of the National Academy of Sciences of the United States of America 20141215 52

The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated ho ...[more]

PMID: 25512547

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Project description:BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST) scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE). METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content) did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST) differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable genome.

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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

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