PONE-D-19-29815

High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor

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Your manuscript has now been seen by two referees, whose comments are appended below. You will see from these comments that the referees find your work of high interest. In light of these comments, only minor revisions are needed - see especially reviewer 2 with the suggestion to move the site description to the supplement.

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Reviewers' comments:

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This manuscript is extremely well written in a very clear and well-organized style. It will require very little correcting, as I failed to find any typos or grammatical errors. The authors are highly qualified, with extensive years of experience in Asian steppe archaeology, focused on the Bronze and Iron Age. The ancient mtDNA, stable isotope and cementum analysis, as well as standard morphological analysis of plant and animal remains form a solid, holistic picture of goat herding in the Djungar Mountains and surrounding regions of Siberia, northern and central Kazakhstan and northwestern Mongolia. The sites from which samples were derived were selected in a meaningful way to capture the evidence to develop their results on subsistence and caprine breeding and maintenance. The sample sizes were ample, although future expansion of data is certainly welcome. Here I would like to briefly summarize their most significant results.

The found that diversity of mtDNA haplotypes was lower for NES sites and higher for IAMC sites, which has major implications for these two regions. They interpret some of the genetic findings as an indication of connections with western China. The absence of B and G haplotypes is interesting and shows the need to increase sample sizes from Iran and China before the migrations of goat populations through Central Asia can be better understood.

One interesting and potentially very significant finding was that morphological identification of wild species of caprines conflicts with their ancient mtDNA results. This casts doubt on previous publications that report hunting of wild species when, in fact, the remains may just be from large males in the domestic livestock. This would mean that hunting was less significant than originally thought, at least for caprines, and that size variation within domestic herds is something worth considering. It could imply that selection for particular characteristics and perhaps even breed development was being initiated in these livestock populations or, as they indicate, the influx of goats from outside after the middle Bronze Age.

Another important development is the assessment of the low frequencies of goats vs. sheep and cattle. This can shed light on the importance of their uses. Goats tend to be bigger milk producers than sheep, and, though the hair of certain breeds is highly valued, sheep would yield wool. The amount of meat they produce is basically the same, so perhaps these populations depended more on cow milk than goat and considered wool production more important than goat hair (if the goats had cashmere or angora-type coats, which is unknown at present-they may have had a short coat).

This paper sheds light on the degree of human population migration owing to pastoral mobility and the bronze trade in the Bronze and Iron Ages. For the NES, there seems to have been less mobility and exchange than in the IAMC. This research marks a significant beginning in understanding connections between human and livestock populations, most notably the activities in Central Kazakhstan as a possible intermediate region, but also a border between the north and south. They interpret the low diversity in the NEC as reflecting the eastward migration of Near Eastern goats from Eastern Europe via the Afanasievo culture (and perhaps others) to the Altai region. The IAMC, on the other hand, was more dynamic, with connections potentially with Iran and China. This exciting research is definitely a great start, but, as they point out, their tantalizing results show that much more work needs to be done in the future to fine-tune our understanding of mobility of herds and people in Central Asia and connections between Eastern Europe, the Near East, and the far East. I look forward to their continuing research and new results and hope that they will also be able to address issues such as breed development and product exploitation (meat, coat, and dairy) through genetic and traditional archaeological information.

Reviewer #2: I think this paper presents novel and interesting data and is professionally prepared and presented. I suggest a few minor changes and reorganizations but otherwise supports its acceptance for publication.

In this paper, the authors present new mt DNA sequences for archaeological (Bronze and Iron Age) goats from two regions 'Central Asia' including the North Eurasian Steppe (NAS) and the Inner Asian Mountain Corridor (IAMC). The authors present mt sequences and haplogroup assignments for 50 domestic goat specimens from 10 sites. This itself is a valuable contribution to the understanding of the historical genetics of goat populations as well as the migration and interaction histories of these two regions. Even more interesting is the patterns the authors identify in the mt data. They point out that goats from the NAS region have low mt diversity, all characterized as mt haplogroup A. In contrast, the goats from the IAMC region reflect higher variation with low frequencies of haplogroup A while also exhibiting haplogroups C and D. From these patterns the authors link the IAMC region with goat diversity on the Iranian plateau whereas the A lineages in the NAS perhaps derive from eastern Europe or the Caucasus region and thus reflect divergent (goat) colonization histories.

These are very interesting data and patterns that fit into the very high profile current discussions of the role of mobility, trade and exchange, and population movements in and through these central Asian corridor regions.

My main concern with reading the paper comes from the organization. I feel like the section describing the sites is intrusive and disrupts the narrative. I suggest moving the site descriptions to a supplement rather than including them in the main text of the paper. I also think it should be easier to identify which specimens represent which haplogroup--this should be included in the main specimen table in Supplement table 1.

Specific and generally minor comments/questions/suggestions:

Line 85: what do the authors mean by saying that mobile pastoralism emerged in the 5th millennium BC? What does ‘mobile’ mean?

Line 102: descriptions of the routes for the spread of domestic animals make it sound like a simple process of migration. Does not address the fact that these regions were occupied by local hunter-gatherers and there are active discussion concerning the mechanisms by which domesticates moved into this broad region.

Line 196-330: this section describing the sites is usually moved to a supplemental file in aDNA publications. I would recommend moving this text and adding a Table to the main text with the site names, dates and perhaps a very brief description of the most relevant details.

Line 365: I am not sure that this sentence is relevant here since it is not referring specifically to

Capra sibirica which, based on Pidancier et al 2006, seems to be a more basal member of the Capra genus, although Sardina et al 2006’s analysis shows Capra sibirica closely related to bezoar and domestic goat lineages. Either way, it is not clear that this comment is relevant unless it is specifically directed at Capra sibirica morphology rather than ‘ibexes’ more generally.

Line 420: lineage D is described as ‘rare’. It is rare based on a study of modern goats in Naderi et al 2007 but based on Daly et al 2018, lineage D is not all that rare—it is present in Neolithic and Bronze Age Iran as well as Chalcolithic Israel. Based on ancient samples in Daly et al 2018 and Colli et al 2015, C is much more rare and is found in wild Iranian bezoar as well as Neolithic domestic goats in the Balkans, modern domestic goats in central Europe, and modern domestic goats in Iran. As a result, C is a less good indicator of the migration direction.

Line 431: Distribution of F is greater than stated here. Based on Colli et al 2015, haplogroup F goats have also been found in wild bezoar in Iran. The authors also report 1 modern Iranian domestic goat exhibiting the F haplogroup (Supplement Table 4). Colli et al 2015 also report that F is also present in wild bezoar from the Caucasus to Pakistan which I think is referencing data from Naderi et al 2008 also report that F is present in modern bezoar populations in southern Turkey and eastern Turkey as well.

Line 475: change wording of “more infrequent” to less frequent

Line 477: this statement is especially true since goats have higher reproductive potential than both sheep and cattle.

Line 521: reword “…while for now…”

Why are the mt haplogroups not labeled in the list of specimens in the Supplemental Tables?

Figure 2: the CKZ label is not identified on the map in Figure 1.

Figure 2: why do the 2 Capra sibirica samples not cluster together? Does this suggest hybridizing with domestic goat populations or just divergent wild Capra mt haplogroups?

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Reviewer #1: Yes: Sandra L. Olsen

Reviewer #2: No

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High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor

PONE-D-19-29815R1

Dear Dr. Hermes,

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