Goat ancient DNA analysis unveils a new lineage that may have hybridized with domestic goats
A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics
The genomic analysis of ancient remains has revolutionized the study of the past over the last decade. On top of the discoveries related to human evolution, plant and animal archaeogenomics has been used to gain new insights into the domestication process and the dispersal of domestic forms.
In this study, Daly and colleagues analyse the genomic data from seven goat specimens from the Epipalaeolithic recovered from the Direkli Cave in the Taurus Mountains in southern Turkey. They also generate new genomic data from Capra lineages across the phylogeny, contributing to the availability of genomic resources for this genus. Analysis of the ancient remains is compared to modern genomic variability and sheds light on the complexity of the Tur wild Capra lineages and their relationship with domestic goats and their wild ancestors.
Authors find that during the Late Pleistocene in the Taurus Mountains wild goats from the Tur lineage, today restricted to the Caucasus region, were not rare and cohabited with Bezoar, the wild goats that are the ancestors of domestic goats. They identify the Direkli Cave specimens as a lineage separate from the
West and East Caucasus Tur modern lineages. Also, analysis of the genomic data and mitochondrial haplotypes reveals hybridization between the Tur and the Bezoar wild lineages. Interestingly, authors also find an uneven amount of Tur ancestry among Neolithic domestic goats, with European domestic goats showing evidence of this ancient Tur ancestry, whereas Neolithic Iranian domestic goats do not, a pattern that is also observed in some modern European domestic goats.
A modified D statistic, Dex, is developed to examine the contribution of the ancient Tur lineage in domestic goats through time and space. Dex measures the relative degree of allele sharing, derived specifically in a selected genome or group of genomes, and may have some utility in genera with complex admixture histories or admixture from ghost lineages. Results confirm that Neolithic European goat had an excess of allele sharing with this ancient Tur lineage, something that is absent in contemporary goats eastwards or in modern goats.
Interspecific gene flow is not uncommon among mammals, but the case of Capra has the additional motivation of understanding the origins of the domestic species. This work uncovers an ancient Tur lineage that is different from the modern ones and is additionally found in another geographic area. Furthermore, evidence shows that this ancient lineage exhibits substantial amounts of allele sharing with the wild ancestor of the domestic goat, but also with the Neolithic Eurasian domestic goats, highlighting the complexity of the domestication process.
This work has also important implications in understanding the effect of over-hunting and habitat disruption during the Anthropocene on the evolution of the Capra genus. The availability of more ancient specimens and better coverage of the modern genomic variability can help quantifying the lineages that went lost and identify the causes of their extinction.
This work is limited by the current availability of whole genomes from modern Capra specimens, but pieces of evidence as well that an effort is needed to obtain more genomic data from ancient goats from different geographic ranges to determine to what extent these lineages contributed to goat domestication.
Daly KG, Arbuckle BS, Rossi C, Mattiangeli V, Lawlor PA, Mashkour M, Sauer E, Lesur J, Atici L, Cevdet CM and Bradley DG (2022) A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics. bioRxiv, 2022.04.08.487619, ver. 5 peer-reviewed and recommended by Peer Community in Genomics. https://doi.org/10.1101/2022.04.08.487619
Laura Botigué (2022) Goat ancient DNA analysis unveils a new lineage that may have hybridized with domestic goats. Peer Community in Genomics, 100020. https://doi.org/10.24072/pci.genomics.100020
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2022.04.08.487619
Author's Reply, 14 Jul 2022
Decision by Laura Botigué, 16 May 2022
The manuscript “A novel lineage of the Capra genus discovered in the Taurus mountains of Turkey using ancient genomics” analyses the genomes of different ~14,000 year-old Capra specimens from an archaeological site in southern Turkey. The time and location of these remains are of interest because they can shed more light into the details behind the domestication process of domestic goats. Both reviewers have found that the manuscript makes relevant contributions in several fields. Reviewer one is particularly enthusiastic about the Dext statistic and suggests that this statistic is exposed in a more relevant manner.
There are however, several concerns that the two reviewers share. The first of them, is that the manuscript revolves around the claim of the novel finding of a lost Capra lineage. Beyond the difficulties surrounding the very definition of species and subspecies that Reviewer 1 raises and the possibility raised by Reviewer 2 of these specimen being a hybrid, both reviewers point to the current gap of knowledge that exists on the population structure of the modern Capra genus. The Discussion should be more explicitly framed acknowledging this gap of knowledge. The second concern is about the processing of the low coverage genomes. Some additional analyses are proposed to avoid mapping biases and to quantify the mismapping effects associated with the low coverage genomes. I also think it would be necessary to provide more information on the number of SNPs used in the different analyses.
Something that the two reviewers do not comment on but I noticed is that in the legend of Figure 1B it is sated that the tree was done for genomes above 0.5x, but Tur2 is included and its genome is reported to be 0.02x.
I think that addressing these points would results in a significantly improved piece of work.