Friday, February 21, 2020

The Testimony Of The Goat

An new paper examining ancient goat Y-DNA and also Y-DNA from modern goats from sixteen different breeds and seven species of wild goats, largely reinforces the paradigmatic narrative regarding the expansion of farming from the Fertile Crescent Neolithic revolution already supported by archaeological and human DNA evidence. 

It turns out that all domesticated goats in the world are predominantly derived from the bezoar goat (a.k.a. bezoar ibex a.k.a. mountain goat) which is native to the vicinity of the forested parts of the highlands of Anatolia (a.k.a. Asia Minor, now mostly in a country called Turkey) and Persia (now called Iran) (more generally "West Asia") where they were one of the first animals domesticated in the Fertile Crescent Neolithic Revolution. As Wikipedia explains:
The bezoar ibex (Capra aegagrus aegagrus), also known as the Anatolian bezoar ibex, Persian ibex, or (by Anatolian locals) dağ keçisi (Turkish: 'mountain goat'), is a wild goat subspecies that is native to montane forests from Turkey to Iran.
The bezoar ibex is found in the mountains of Asia Minor and across the Middle East. It is also found on some Aegean islands and in Crete, where it is accepted that the goats constitute relict populations of very early domestic animals that were taken to the Mediterranean islands during the prehistoric period and now live as feral populations. The bezoar ibex, if not the sole progenitor of the modern domestic goat, is at least its main progenitor. The archaeological evidence traces goat domestication as far back as c. 10,500 years Before Present, and DNA evidence suggests 10,000 years BP.
In particular, the geographic distribution of goat Y-DNA shows the distinction between the LBK and Cardial Pottery waves first farmer migrations. It also shows a separate wave of goat herding migration with a different mix of lineages than in Europe, that were likely spread across Africa via the Egyptian Neolithic.

A more notable finding is that almost all domesticated South Asian, Southeast and East Asian goats, other than those arriving within the  modern era (i.e. starting no earlier than last five hundred years or so, and perhaps even in the 20th century) in Korea and Japan, appear to be derived from lineages (some of which are rare in Europe and Africa) of Fertile Crescent Neolithic Iranian goats, rather than deriving from an independent domestication. This indicates that economically significant long distance trade between West Eurasia and East Eurasia at some point in the prehistoric Holocene era. The exact timing can probably be accurately estimated based upon the time at which remains of goats are first attested in these places, but that data isn't available in this particular paper.

Another interesting point is that while Madagascar was settled by a population of mixed East African and Indonesian origins, its goats all have African origins, even though its language is almost entirely Indonesian (and Austronesian) in origins. This adds another data point to the unclear question of what the nature of the relationship between the Indonesian and East African founders of Madagascar had with each other.

It is also rather remarkable how long an imprint of Neolithic migrations seem to have endured pretty much worldwide, despite significant global trade that goes deep into prehistory. The immense turnover of human populations in the Bronze Age in Europe and Southeast Asia, and in the Bantu expansion in Africa, appear to have overlooked goats.

The new preprint about this topic and its abstract are as follows:
The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species.  
We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.
Isaäc J. Nijman, et al., "Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats" bioRxiv (February 17, 2020) doi:

From the body text (citations omitted):

A preliminary analysis of the Y-chromosomal diversity in European and Turkish goats defined the three haplotypes Y1A, Y1B and Y2, showing strong geographic differentiation. The same haplotypes were found in goats from Portugal and North-Africa, Turkey, east and south Asia, Switzerland and Spain with additional haplotypes Y2B in east Asia, Y2C in Turkish Kilis goats, and Y1B2 as well Y1C mainly in Switzerland. . . . 
Remarkably, with the exception of Y1B the haplogroups have all been found in Iranian bezoar samples, whereas all haplogroups, including Y1B, were detected in ancient goat samples. 
Geographic plots of haplogroup frequencies show a considerable spatial differentiation, which resonates the strong phylogeography displayed by autosomal SNPs, but is in clear contrast with the phylogenetic structure displayed by mtDNA haplogroups. Most likely, by a series of bottlenecks in the male lineage subcontinents have different major haplogroups, while none has a global-wide coverage:

- Haplogroup Y2B is absent in Europe, Africa and west Asia, but became a major haplotype in east Asia and southeast Asian, where Y2A is not represented. In contrast, it is observed in ancient goat from Medieval Georgia and Neolithic Iran (ca. 6,000 BCE), supporting an origin of east Asian goat from regions east of Zagros Mountains.

- Y2A is in northern and central Europe only found in the crossbred AngloNubia, but is the predominant haplogroup in central, eastern and southern Africa.

- Haplogroup Y1B is predominant in northern Europe, but outside Europe and North African has only been found in one Karamonja animal, in the Korean native breed and in exported Saanen populations. 
The different Y2A and Y1B frequencies in north-central vs southern Europe may reflect the Neolithic migrations following the Danube and the Mediterranean routes, respectively with the strongest bottlenecks along the northernmost migrations.

- Y1AA is sporadic in Europe and has been observed also in Neolithic Serbia (ca. 6,000 BCE), but is present in Asia. 
Deviations from the general pattern may very well reflect major introgressions. A well-known example is the Anglo-Nubian, which originated in England by crossing Indian or African imported goats with local breeds and is in our panel the only northern-European breed carrying Y2A. 
There were two out-of-range findings of Y1B, in the Uganda Karamonja and in the Korean native breeds. Because of the popularity of Swiss dairy goats in both Uganda and Korea, crossbreeding again is the most likely explanation. 

Fig. 2.
Haplogroup distributions of (A) European breeds; (B) Asian breeds; (C) African breeds; (A, B), European and Asian ancient DNA samples; and (B) Iranian bezoars. 
Breeds represented by a single goat are not plotted or are combined with other breeds from the same country. 
Breed codes: ABA, Abaza; ALP, Alpine; ANB, AngloNubian; AND, Androy; ANK, Angora;Ankara; APP, Appenzell; ARA, Arabia; ARG, Argentata dell’Etna; ARR, Arran; ARW, Arapawa; BAG, Bagot; BAL, Balearic; BBG, Black Bengal; BEY, Bermeya; BHU, Bhutan; BIO, Bionda dell’Amadello; BLA, Blanca Andaluzza; BLB, Bilbery; BLO, Blobe; BOE, Boer; BRA, British Alpine; BRV, Bravia; BUK, Polish Fawn Colored; CAM, Cambodja; CAP, Capore; CHN, North China (Xinjiang, Henan Raoshan White, Shandong); CHQ, Charnequeira; CHV, Cheviot; COR, Corsican; CRO, Croatian Spotted; CRP, Carpathian; DIA, Diana; DJA, Djallonke; DKL, Danish Landrace; DPG, Dutch Pied Goat; DRZ, Dreznica; DUK, Dukati; DUL, Dutch Nordic Goat; ESF, Esfahan; ETH, Ethiopian (Abergelle, Gumez, Keffa); FIN, Finnish; FLR, Florida; FUE, Fuenteventura (Ajuy, Majorera); GAL, Galla; GAR, Garganica; GDR, Guadarrama; GGT, Girgentata; GMO, Grigia Molisana; GRG, Greek; GRS, Grisons Striped; GUE, Guéra; GUR, Gurcu; HAI, Hair; HAS, Hasi; HNM, Honamli; IND, Indian; IRA, Iranian; JPA, Shjiba; JSA, Japanese Saanen; KIG, Kigezi; KIL, Kil; KLS, Kilis; KMO, Karamonja; KON, Korean Native; KSA, Korean Saanen; LAO, Laos; LBA, Lori-Bakhtiari; lCL, Icelandic; LIQ, Liqenasi; MAK, Makatia; MAT, Mati; MAU, Maure; MEN, Menabe; MGL, Mongolian; MLG, Malagueña; MLI, Naine, Soudanaise Targui; MLT, Maltese; MLW, Malawi (Balaka-Ulonge, Dedza;Lilongwe; MOR, Moroccan; MSH, Mashona; MTB, Matebele; MUB, Mubende; MUG, Murciano Granadina; MUL, Mulranny; MUZ, Muzhake; MYA, Myanmar; MZA, M’Zabite; NCG, Norwegian Coastal; NDG, Norwegian Dairy; NDZ, Norduz; NGD, Nganda; NKA, Naine de Kabylie; ORO, Orobica; PCG, Peacock; PEU, Peulh; PHI, Philippines; PIZ, Pinzgauer; PYR, Pyrenean; PYY, Payoya; QHI, Qinhai; RAS, Rasquera; ROV, Rove; RSK, Nigerian Maradi (Red Sokoto); SAA, Saanen; SAR, Sarda; SCA, Shaanbe Cashmere; SDN, Sudan; SEA, Small East African (Kenya, Uganda); SEB, Sebei; SRP, Serpentina; SER, Serrana; SGB, St Gallen Booted; SHL, Shahel; SHL, Nigerian Sahel; SKO, Skopelos; SOF, Sofia; SOU, Southwest; SSG, Steirische Schecken; TAS, Tauernschecken; TER, Teramo; TIB, Tibetan; TNF, Tinerfena (Norte, Sud); TOG, Toggenburg; TWZ, Thuringian Forest; VAL, Valdostana; VBN, Valais Blackneck; VIE, Vietnam; VRT, Verata; VZC, Verzasca; WAD, West African Dwarf; ZAR, Zaraiba.


DDeden said...

I'm being pedantic, but my jaw dropped when I saw "West African Dwarf". The appropriate term is surely "West-Central African Pygmy". Dwarf indicates relatively short limbs vs torso & head, Pygmy indicates proportionately normal limbs vs torso & head.

DDeden said...

As I am apparently. Can you administratively delete my comments here?

andrew said...

I can. But, don't fret it.

DDeden said...

Thanks. I don't mind my typos, minor errors, speculations being recorded for posterity (or whatever), but diverting attention of readers from your post message wasn't my intent.