October 28, 2015

Irish and British cattle may have greater wild auroch admixture

Quickies

Stephen D.E. Park et al., Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biology 2015. Open accessLINK [doi:10.1186/s13059-015-0790-2]

Abstract

Background

Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals.

Results

Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle.

Conclusions

This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

Fig. 5. Geographic contour map of aurochs genomic admixture with individual European breed D statistics (ABBA/BABA test results) plotted according to population origin and visualized using the ArcMap component of the ArcGIS software suite. The ABBA/BABA test tree topology is also shown and the contour point value for each European breed (P1) was generated from the mean D statistic where P2 is set to each of seven West African taurine populations in turn

17 comments:

  1. They need to sample Iberian cattle (including wild cattle) for comparison. I suspect that these also have a high level of Auroch ancestry, and that the ancient British and Irish breeds of cattle derive a large portion of their ancestry from Auroch-admixed Iberian cattle due to neolithic &/or bronze age migrations.

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  2. I agree that sampling Iberian cattle is a necessary complement. I don't agree that it will necessarily produce results similar to those of the islands or that the breeds are related necessarily.

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  3. Well, by the title of this topic («Irish and British cattle have greater wild auroch admixture»), a person can lead to think that the scientific research paper is providing definitive evidence for that when it isn´t. What was found is that local British aurochs was involved in the formation of some British local landraces. I have found this very interesting, plus it mentions which breeds and sheds some light on how it happened. But the authors are cautious when they mention this: «In addition, future analyses of whole-genome sequences from modern animals and additional aurochs samples will refine the catalogue of genomic loci that contribute to key functional traits in domestic cattle.»

    «The presence of putative B. primigenius P, R, Q and, most recently, C mtDNA haplogroups in modern and early domestic cattle populations from Europe and Asia has provided some support for the local domestication of wild aurochs females in Europe.»

    Q was found, at least, in some Portuguese and Italian Breeds. P was found in Korean Beef cattle. Probably more aurochs mtDNA lineages will be found in domestic breeds, as studies progress.

    « The British CPC98 aurochs specimen is an outgroup—with 100 % bootstrap support—to the entire modern B. taurus clade in this phylogeny. This is corroborated by the principal component analysis plot shown in Fig. 3 in which CPC98 is peripheral to the European B. taurus sample group along principal component 1. These results provide strong support for the hypothesis that the North European aurochs is an evolutionary outgroup to all domesticated taurine cattle»

    This is what should be expected and it´s supported by previous studies: Southern European aurochs seem to be closer to domestic cattle/Middle Eastern aurochs, not to Central European aurochs, which seem to be really distinct.

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  4. By the way, regarding Y1, there´s a relatively recent study that points this Y-DNA as evidence of aurochs bull introgression:

    http://pendientedemigracion.ucm.es/info/prodanim/html/JP_Web_archivos/64.pdf

    Like in pages 11,12 and 14.

    If so, Iberian breeds (both Spanish and Portuguese), Northwestern and Western European breeds, at least, have this influence. But it could exist more, I don´t have all the data with me now.

    I know that this Y1 subject have had some changes. Firstly was thought to be really from the European bull aurochs, later as a mutation that happened in domesticated cattle and on this paper is considered to be bull aurochs influence again.
    Maybe the authors of this British paper, were still basing on the second theory and were unaware of the latest findings, but I´ll try to confirm this.

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    1. Your insight is very appreciated. I admit I don't have an opinion myself, so learning from what you say, thank you.

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  5. This is the actual name of the article: «Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.»

    And nowhere it says there that is Irish and British cattle that have greater wild auroch admixture.

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    1. It clearly says so: "Figure 5 shows a contour map of the individual European breed D statistics plotted according to population origin. These results provide compelling evidence supporting the hypothesis of a significant genetic contribution from British aurochs to modern domestic cattle populations from Britain and Ireland".

      There's other data like fig. 6, etc.

      As for the title, I copy-pasted it and it seems to be correct, so I'm not sure which is your problem. Are you trying to make me work in vain or something?

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  6. Having in mind the already proved big amount of aurochs genetic variation on its widespread geographic distribution (plus belonging to 3 different subspecies), to say that British and Irish cattle breeds are the closest to the aurochs, is a «bit» overgeneralizing, to say the least.
    What is implied is that the British aurochs had a significant contribution to some local breeds, not that these breeds are the ones that have greater wild aurochs admixture.
    It would be like saying that the Ari people are the ones that have greater hunter-gatherer admixture (when that statement would be only based on the Mota remains).

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    1. Are you saying that wild European aurochsen are not an outgroup relative to domestic Bos taurus of mainly West Asian origin? Are you saying that, if we'd take a wild auroch from somewhere else, say Romania, it would work differently? Which is your evidence? Or is it just a wild guess?

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  7. Hi, and nice blog.

    What we show in the paper is that British and Irish cattle have a greater degree of genes in common with a British aurochs sample, presumably through introgression. We don't know yet what would be the findings if you repeated the analyses using an aurochs genome from a different region of Europe. Possibly Italian breeds would be shown to derive a portion of their genome from aurochs populations from south of the Alps. This might account for some of the rare mitochondrial haplotypes found there.

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    1. Thank you for the compliment but especially for the clarification, Stephen. I guess I will have to slightly alter the title and add the word "may", so everybody is happy. :)

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  9. What´s so difficult to grasp for you (no one is here to be happy)?
    That not all aurochs are the same? Just google it and you´ll find 3 different subspecies. Plus within taurine group (North African and Eurasian) there was a great deal of diversity. Even the so-called traditional domestic T3 haplogroup, was found apparently in many Italian aurochsen (being P a minority), so this only tells about how complex this subject is and how we are still on the beginning.
    And your change doesn´t alter s big deal because you are still losing the main point, like Stephen (and even Geog marin) had the attention to explain to you: «What we show in the paper is that British and Irish cattle have a greater degree of genes in common with a British aurochs sample, presumably through introgression.»

    Basically you have to be more precise about which aurochs exactly you mean (even within each subspecies there was a great deal of diversity).
    All we know from this paper is that a British aurochs individual/sample have greater degree of genes in common with some British and Irish cattle breeds, than any other breeds. I would say that probably introgression is the reason.
    Although this is your blog, you shouldn´t make suggestions that people are here to see things like they want.

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    1. Why are you so confrontational? I'm not even analyzing the study, just referencing it, so, sure, feel free to post your opinion on the matter but, instead of trying to forcibly convert me to your ideas (so clear in your mind but so poorly expressed outside it, it seems), why don't you try to explain, with less aggressiveness and more documentation (instead of "just google it", try posting one or several relevant links, with more pedagogic explanations, maybe a quote...)

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  10. Don´t try to act as a mind reader/guesser and I would suggest you to focus on what has been said to you.
    And I don´t need to quote what´s on the study already and what Stephen and geog already explained to you. If you want still to ignore that, that´s up to you.

    One last suggestion for your title: «Irish and British cattle may have greater British wild aurochs admixture».

    Reason: Simply because this is what is implied on the study, this is what this study is about, this is the evidence that we have now and not something else.
    Now do as you want.

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    1. Fernando: Do NOT come to MY BLOG (= my space, my home, my turf) trying to give me orders or being disrespectful. You get a warning this time: if you want to retain your CONCESSION to be able comment, reform your attitude, please. Thank you in advance.

      Your suggestion comes late anyhow, as I already changed the title but because of the explanations of lead author Stephen Park, see his comment above and my reply, not because you try to be bossy with me.

      The permalink retains the name of the old title but that's because it was generated automatically with the first edition. I can't reform that.

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    2. This comment has been removed by the author.

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