I finally had the time to finish a lengthy post with lots of literature references – the complete (as far as we know to date) genetic history of the species of aurochs and cattle, Bos taurus. To explain why I now use Bos taurus for this species instead of Bos primigenius. I know opinion 2027 does enable the use of nomina of wild animals that are predated by names for their domestic counterparts, but this regulation does not apply in this case, because Linnaeus described not only taurine cattle but also the aurochs under this name in 1758 (“ferus urus”). Therefore, I use Bos taurus for the entire species. It could use a lectotype though.
The position of aurochs and cattle on the tree of life: The Bos clade
Since there is no clear definition of a species that works universally, and the transition from a species to its ancestral species is fluid, I borrow a method from phylogenetic systematics for my definition of an aurochs: everything that evolved from the last common ancestor of both extant aurochs lineages (taurine and indicine) is a crown-group-aurochs, everything that is closer to an aurochs than to its closest living relatives (bison, yak, gaur, banteng, kouprey) but is not a crown-group-aurochs is a stem-group-aurochs. For example, the Haßleben aurochs, which can safely be assumed to be closer to taurine cattle than to indicine cattle due to its location, age and morphology, would be a crown-group-aurochs. The Wadi Sarrat cranium would most likely be, because of its geological age, a stem-group-aurochs. The immediate ancestor of Bos taurus would be a stem-group-aurochs too, unless Bos taurus derived right from the LCA of the entire Bos clade. This may sound impractical, but it is the only clear-cut solution, because if the primigenius-type aurochs indeed evolved from the Siwalik ox Bos acutifrons with over a transitional form, it is impossible to draw a clear line between the species that is extant now (but not in its wildtype) and its ancestral species, especially as we do not know how to properly define a species. Dealing with clades is much more definite in this case.
Having defined what I mean by “aurochs” for the purpose of this article, let’s look at its place among its closest living relatives within the Bos clade. This clade includes aurochs, yak, kouprey, bison, banteng and gaur. These species seem to have radiated in a short period of time, very likely accompanied by hybridization and incomplete lineage sorting. As a result, different markers result in different phylogenies for that clade. I listed some of them in my book Breeding-back wild beasts: aurochs, wild horse and quagga. Y chromosome markers, nuclear autosomal genes and mitogenomes all result in different phylogenies. Hassanin et al., 2013, estimate based on nuclear data that the major diversification of the Bos clade took place in the Pliocene, 3,75 million years ago [1]. The recent radiation of the Bos bovines is also evidenced by the interfertility of the species – a sometimes more, sometimes less limited interfertility, I should say. Because of the recent, rapid and multifaceted diversification of the Bos species it might be a case were morphological can provide helpful clues, and they do seem to agree with taxa that have been found relatively robustly in genetic analyses: yak group with bison (and could be placed in together in the subgenus Bison), kouprey, banteng and gaur group together in most phylogenies (and could be placed in the subgenus Bibos), aurochs and its domestic derivatives are either sister to the other species or group together with the Bibos species. In order to get an overview over the phylogenies performed with the Bos clade, see [1, 2, 3, 4, 5, 6].
There is unfortunately no genetic data from fossil taxa that could be highly relevant, such as Bos acutifrons, Bos buiaensis, Pelorovis (? Bos) olduwayensis or the Leptobos taxa (some of which do have a clear primigenius spiral, but often absent horns in females). It should be noted, though, that B. buiaensis and B. acutifrons have very similar, extremely wide-ranging horns that are proportionally about as large as in early aurochs but barely curve inwards. The postcranial skeleton of both taxa is, as usually with fossil bovines, not properly described. Both species are not only very similar in horn shape, they are also from about the same time of around two million years ago, albeit different continents (northern Africa in B. buiaensis, Siwalik hills of India in B. acutifrons). I would not be surprised if both are variants of the same bovine species with extremely wide-ranging horns that had a transcontinental range (this is not unusual for bovines, think of aurochs or bison).
Aurochs from deep time and the mess with Bos namadicus
Both B. buiaensis and B. acutifrons have been suggested as the ancestral species of aurochs. If both species are closer to the crown-aurochs than to other living bovines, they would be stem-aurochs. Without any genetic data and a rigorous analysis of their skeletal morphology, we cannot say much about that. However, the oldest record of the aurochs that is know so far is the Wadi Sarrat skull from 770.000 years ago, North Africa. Is this one a stem-aurochs or a crown aurochs? What about the fossil remains assigned to Bos namadicus? Is this the ancestral form of zebu or even all other types of aurochs, as van Vuure (2005) suggested?
There are two extant lines of the species of aurochs: indicine cattle and taurine cattle. Their separation would define the lifetime of the first crown-aurochs, the first “modern” aurochs. It is well established that they separated within the wild populations, and all analyses so far point to a separation in well in the Pleistocene. But the exact date of that event is hard to pinpoint.
Molecular clock estimates are model-dependent and also rely heavily on fossil calibration and the fossil record is, as we all know, incomplete. Also, different markers can give different results because of divergent coalescences. It is known, for example, that mitochondrial markers can result in much older estimates than autosomal markers. Early studies such as Loftus et al [7], Bradley et al. [8], MacHugh et al. [9] and Hiendleder et al. [10] worked with mitochondrial data and found a divergence between the taurine line and indicine line deep in the early Pleistocene at one million, two million or approaching one million years ago. More recent studies, using nuclear SNPs found much more recent dates, such as Burt et al. [12], according to who they separated around 250.000 years ago or Ward et al. [14] with 150 to 500kya. Verdugo et al. [13] and Rossi et al. [15] included aDNA samples of wild aurochs and ancient cattle and found a time of divergence at 200kya and 166-300kya, respectively.
When Rossi et al. (2024) was published, I wrote that most well-known fossils assigned to Bos namadicus therefore predate the split of taurine and indicine cattle, thus they could not be representatives of the line leading to zebus. However, there are cranial similarities between Bos namadicus fossils and indicine crania that distinguish them from European aurochs and taurine cattle, which seems contradictory. If zebus and taurine cattle are closer related to each other than zebus to namadicus, this should not be the case.
However, the solution to this mystery might be twofold: 1) the accuracy of molecular clock estimates is not carved in stone and 2) most, if not all, namadicus fossils are not dated directly. Pleistocene fossils assigned to this taxon are for example from the Narmada valley and other formations that cover a time from roughly 700.000 to 100.000 years ago. This is where the age estimates for namadicus comes from, but its fossils usually are not dated directly. So, given that molecular clock estimates cover a range of several hundred millennia and so does the possible age of namadicus fossils, it could well be that most fossils of namadicus, the bulk of which are from the late Pleistocene, could be from after the divergence of the indicine line and the taurine line.
Thus, notions that Bos namadicus is from 700kya have to be taken with a huge grain of salt. The dating of the Wadi Sarrat cranium was not direct either, but covers a far smaller range due to biostratigraphy. This cranium shows the more familiar aurochs craniotype: broad and slightly concave frontal area, protruding orbital bosses, wide-ranging forward-facing horns. Not only is this one the oldest record of aurochs that is more or less reliably from 700kya, it also suggests that it is really the namadicus type that is the deviant one from the ancestral form. So the assumption by van Vuure (2005) that the Indian aurochs is ancestral to all the other forms of aurochs, seems to be the other way round: the Indian type is the more recent, more derived form and zebus are the pinnacle of that.
Does it make sense to divide predomestic mainland Bos taurus into subspecies?
The classic subspecies scheme has three mainland subspecies of wild Bos taurus: the European subspecies (primigenius), the Indian subspecies (namadicus) and the African subspecies (mauretanicus). Rarely noticed is the East-Asian one (suxianensis). The idea would have been that from the origin of the aurochs, the regional subtypes would have colonized their regions and followed an own evolutionary path, i.e. that a North African aurochs from 100kya would be closer to a North African aurochs from 8kya than to a European one from 100kya and so forth. This idea is, as we now know through genetic data, outdated and simplistic.
The most important work in this regard is Rossi et al. 2024. They analyzed 38 wild aurochs genomes, all of which are not older than 50.000 years, and found that wild aurochs were subject to repeated expansions and contractions of their range, possibly as a result of the dramatically changing climates of the Pleistocene, and that the populations form a much more complex tree than thought earlier. The earliest split was that between the lines of taurine and indicine cattle at around roughly 200kya (zebu were used as a proxy for namadicus in this study, of which no genome was recovered yet). Then, after 100kya, the taurine line split up between North Asian aurochs and a more western clade. That one includes Southwest Asian (Near Eastern) aurochs, European aurochs and North African aurochs belonging to haplotype R. The most recent glacial maximum at around 25kya led to another split between European and Southwest Asian aurochs. European aurochs further evidenced signs of introgression from local much older aurochs in Europe, belonging to haplogroup G from around 390kya. These are the outgroup to all other aurochs lineages recovered, including zebu. This means that old European skulls, such as the ones from Madrid at around 600kya, are less close to taurine cattle and late European aurochs than zebu are – and provides further clues to the assumption that the deviant namadicus aurochs evolved from the classical primigenius morph, not the other way round.
After the end of the most recent glacial, North Asian aurochs of the C and K haplotypes started to show intermixing with European haplotypes such as P and Q, most likely as the range of the bovine expanded with the warming climate [15].
What is important to note is that all this was derived from relatively recent genomes, as we do not have older genomes yet – the story of expanding and contracting populations and the splitting off of lineages from each other probably also was the case in much earlier aurochs, for which we have no data yet. That means that the 770.000 years old Wadi Sarrat cranium from North Africa is definitely not from the same evolutionary line as late Pleistocene aurochs from Africa, such as the skull from the Ouran caves. These are rather much closer to late Pleistocene European and Southwest Asian aurochs, including taurine domestic cattle, while the Wadi Sarrat cranium is equally distant to taurine and indicine cattle.
Interestingly, not only did Park et al. (2015) find that zebus share alleles with the European aurochs genome that taurine cattle do not have, Rossi et al. (2024) found deep alleles that zebus share with the bovine outgroups gaur, banteng, wild yak and wisent, that taurine cattle and western aurochs do not have [15].
This means that upholding the old aurochs subspecies scheme makes no sense for mainland populations. The evolution of wild aurochs populations was much more dynamic. My suggestion is to abandon the subspecies names for mainland aurochs lineages, with the possible exception of namadicus – in the case of namadicus, we seem to have a separated line in one region that also was morphologically quite distinct. The Iranian deserts [17] to the west and the Himalaya to the North probably limited gene flow between namadicus and other aurochs populations. This might explain why it was so deviant.
Another case where a subspecies status makes sense are the insular forms siciliae, bubaloides and thrinacius, because we are dealing with clearly reproductively isolated populations that were also morphologically distinct.
All haplotypes found within Bos taurus
Haplotypes are important for the study of genomic evolution as they reveal genealogical patterns: splits, introgression, migrations, founder events, loss of lineages et cetera. Mitochondrial haplotypes found within Bos taurus, wild and domestic, are as it follows:
T1-5: Most domestic cattle have haplotypes of the T haplogroup. T3 is the most common variant among European taurine cattle and their descendants in the new world, T2 is dominant in the Near East but also found in some Eastern European breeds, particularly from the Balkans [20] and T1 is almost fixed in African taurine cattle but also present in some Iberian and Criollo breeds [19]. T4 is nested within T3 and common in Turano-Mongolian breeds. T5 is very rare and found in breeds such as Piemontese and Valdostana. It was once believed that Italian aurochs also had the T3 haplotype, nowadays it has been reclassified to broadly T [18].
P: The typical haplotype of Late central- western- and northern European aurochs [21]. It is found occasionally in domestic cattle, most notably in Japanese shorthorn in a high frequency of 45,9% [21].
Q: One of the foundational taurine haplotypes from the Near East but rare today [22]
E: Another haplotype found in European aurochs, but not nearly as common as P [23]
R: A haplotype today found in Italian cattle, but possibly of North African aurochs origin as it was found in an African aurochs [13]. Iron age cattle from Tunisia were also found to carry R [24]
G: The old European aurochs haplotype that is basal to all other known haplotypes, as already mentioned. Extinct.
K: This haplotype was found in North Asian aurochs from Kazakhstan. Extinct.
C: The sister lineage to the K haplotype on the North Asian clade that might need to be split up in several haplotypes [25]. Extinct.
I1-2: The two indicine haplotypes. They are not separated by breeds, most breeds have both of them at different frequencies. Due to intermixing, 1,3% of European taurine cattle have indicine haplotypes [26]
The Y-chromosomal diversity recovered so far is much lower, which is to be expected considering the reproductive system of cattle were a few dominant bulls cover most of the cows most of the time. The haplotypes recovered so far are:
Y1: Mostly found in Northern and Northwestern European cattle, but also in a Neolithic aurochs from Bulgaria [15]
Y2: Found in a Neolithic aurochs from Sweden and cattle mostly from Central and Southern Europe, Near East, Africa and parts of Asia [27]
Y3: The one and so far only indicine Y-chromosome type
Y4: Found in East- or North Asian aurochs [28]
There are also subtypes such as Y2a and Y2b, predominantly in Asian cattle, and due to repeated intermixing some Chinese cattle have both Y2 and Y3 [29]. African Sanga cattle, of which the most famous representative is Watussi, are mitochondrially taurine, paternally zebu [19].
Hence, the most prevalent Y-chromosome types found in taurine cattle were already present in Western Eurasian aurochs during the Neolithic. Whether or not Y3 is originally from namadicus can only be speculated as we have no aDNA from this form. The Y4 lineage seems to be lost altogether.
The domestication of cattle
At the very beginning of the Holocene, two important new clades of the aurochs were established. They differ from all the other aurochs clades in being created from human hand, more or less (in earlier times much less) separated from the other populations, being subject to artificial selection by humans.
The first domestication event created taurine cattle in the Fertile Crescent. Archaeozoological evidence points to a domestication in the context of the pre-pottery Neolithic culture of south-eastern Anatolia [30, 31]. Genetic data agrees with this, finding roughly 80 initial maternal founders [27]. 80 cows is an estimate that is compatible with the maternal diversity found in the later domestic cattle pool, it is derived from the mitochondrial diversity. Taurine cattle arrived around 9000 BP in Europe, via the Balkans [32]. They arrived in North Africa around 1000 years later than that [33].
There have been multiple attempts at demonstrating local domestication of aurochs in places such as Iberia, Italy, the Balkans, Siberia or North Africa, but none of them succeeded. Rather, it seems that influence from local aurochs came via introgression from wild populations rather than independent domestication, but more on that later.
There was, however, at least one other domestication event, concerning namadicus. That zebus have a separate origin has been genetically demonstrated unequivocally in 2010 [34], although already Linnaeus described the zebu as a species separate from taurine cattle and aurochs, Bos indicus.
Mehrgarh in Pakistan has the earliest evidence of cattle domestication in Southern Asia at around 9500 years BP [35]. Chen (2010) speculated that I1 and I2 indicates two separate domestication events, while Perez-Pardal et al. (2018) suggest that I2 stems from later incorporation of further wild matrilineages [36]. Pitt et al. (2018) rejects a third domestication event [37].
The dispersal of domestic taurine cattle from then-fertile Southwest Asia to many other parts of the world required local adaptions, which the cattle received via introgression from indicine cattle as much as local aurochs. According to Verdugo et al. (2019) the cattle nowadays in the Near East are not representative of the original basalmost domestic taurine cattle but have been crossbred extensively with indicine cattle during the Bronze age [13]. This was the time of the 4,2kyr climate event, when a sudden drying of the region made adaptions to droughts necessary, which were delivered by zebus that originate from tropical and seasonally arid Southern Asia [13].
Another region where taurine cattle seemingly received local adaptions through introgression was Northern Africa. Breeds from this region, such as N’dama, are famous for their trypanotolerance, which is neither found in non-African taurine cattle nor zebu [38], and thus might be inherited from local African aurochs, which we know influenced early African Bronze Age cattle [23], with lineages carrying R haplotypes till today.
The snowy winters of Europe with different pathogens also required adaptions of the taurine cattle that arrived from the Near East. That local European aurochs left a genetic trace in European cattle is now well-established [39, 40, 41]. Unfortunately, it has only been established that introgression happened but not what kind of adaptions it transferred on European cattle. I would not be surprised if immunological and coat adaptions would have been among them, especially the somewhat woolly coat of many British landraces, which we know to have experienced local aurochs introgression [39], is a legacy of interbreeding with wild populations in Europe.
But also Eastern aurochs left a trace in the modern cattle gene pool. Albeit no Y4 or mt haplotype C persisted to this day, early domestic cattle from China were about 10% influenced by Eastern aurochs [28]. A genetic connection between East-Asian and, surprisingly, Hereford, has been found [46].
Introgression between wild and domestic Bos taurus was not a one-way-street, though. The gene flow went in both directions. As soon as domestic cattle arrived in Europe, aurochs and cattle intermixed [41]. Early Iberian cattle were heavily influenced by local aurochs and from about 4000 BP the local aurochs influence stabilized by around 20% [41]. The gene flow was many from wild bulls to domestic cows, which explains why the introgression was not detected until nuclear DNA was investigated: if a wild bull covers a domestic cow, the offspring will be domestic on mitochondrial DNA, and if the hybrid bulls are culled because of their behaviour or any other reason, and only hybrid cows are kept for further breeding, the subsequent hybrid offspring will have domestic Y chromosomes and domestic mt DNA. What was novel in the study by Günther et al. is that morphologically aurochs-esque remains were found to carry more or less significant portions of domestic DNA [41]. This is not surprising, however, considering that wild boar, wolves, horses and other wildtypes are often introgressed by neighbouring domestics and there is no reason to assume bovines are different in this regard. I think that the domestic intermixing also influenced the morphology of some European aurochs, as late European aurochs were the only wild populations where smaller-horned individuals started to appear, such as the Önnarp aurochs or a very small-horned possibly female skull from a cave in the French district of Bauges.
Going eastwards, also non-aurochs species left a trace in the domestic Bos taurus pool. Chen et al. (2018) found that southern Chinese cattle are 2,93% banteng and Tibetan cattle 1,22% yak [42]. Chen et al. (2023) even found banteng and gaur introgression up to numbers as high as about 10% in Southeast Asian indicine cattle [43]. Indicine cattle also left a strong genetic trace in domestic gaurs [44]. Domestic cattle introgression has also been found in domestic yaks [45]. I think this mutual hybridization, albeit human-facilitated, shows how closely related the only recently diverged Bos species complex is.
Genes possibly affected by domestication
Domestication has a profound genetic impact. First of all, it starts with a dramatic genetic bottleneck. What then follows is massive directive selective pressure, since those bovines that cope better with being under human husbandry and that are easier to handle will be kept for further breeding. Then there is also relaxed selection on traits that are important for a survival in nature that are no longer selection criteria, such as acuity of senses, camouflage, horn shape and size, sexual dimorphism et cetera.
Clearly, domestication must have influenced a large number of genes; new mutations arose, and if advantageous in the new environment, they were positively selected for and the corresponding wildtype alleles disappeared. But also the bottleneck event and the targeted selection must have changed the genetic make-up of the animals in reducing the heterozygosity of the genome, making rare variants either disappear or suddenly become fixed. This alone might have influenced the phenotype of the earliest domestic cattle.
Do we know which genes in particular were subject to profound change during domestication? There are a couple of studies providing some clues. Park et al. (2015), when presenting the first genome of a Neolithic male aurochs from Britain, broadly mentioned that domestication seems to have influenced neurobiology, growth, metabolism and immunobiology [39]. Two years later, Braud et al. found some specific candidate genes. To be precise, they did not look for different transcribed proteins, but rather the regulation of the proteins – the regulation of gene expression rather than a change in the actual proteins was likely highly relevant during domestication. They compared the genomes of cattle and the British aurochs bull and found more than 1.600 protein-coding genes with altered miRNA binding sites. These mutations do not change the protein itself, but can intensify, reduce or terminate the translation of the protein. The function of these genes does fit what we would expect to have been important during domestication: immunology, metabolism, growth and development, neurobiology and behaviour, reproduction and economic production such as milk and meat quantity or quality [47]. A neurobiological gene, among many others, that has been found to have an altered expression in cattle compared to in aurochs is the PHYHIP gene [39, 47].
Despite these studies, no particular genes have yet been identified that may have played a key role in early domestication or would be key targets for genome editing if one was to edit cattle to be more aurochs-like. But I think that based on Braud et al. as much as on how vertebrate organisms function, a very large number of genes must have been involved during domestication.
Which cattle breeds are closest to the aurochs?
This is of course the million-dollar-question for “breeding-back”. But quite honestly, I would be surprised if any cattle breed or population is closer to the aurochs on key genes (that is, those that have a significant influence on phenotypic aspects such as morphology, development, immunology etc.) to a meaningful extent. The gene flow between wild Bos taurus and their domesticated derivates ceased that long ago that I think any wild traits delivered by introgression have been more or less stabilized and distributed evenly among most cattle breeds of the respective regions.
Many of you will know the Nei distance chart published by Rewilding Europe in 2015. I did a couple of posts in the past on why I think this chart does not tell us much since I think a Nei distance of 700.000 SNPs is not the right tool to determine which breeds are “closer to the aurochs”, i.e. less derived, than others. One important aspect is that only one genome of the aurochs was used as a reference, which is surely not enough to cover the diversity of the wild populations. This bears the danger that wildtype alleles preserved in cattle are not recognized as such because they are not present in that one particular genome of the aurochs we had at that time. This would highly skew the results.
Another problem is that a Nei distance of 700.000 SNPs only tells us about closeness of the investigated cattle breeds to the aurochs on exactly these SNPs, but virtually nothing about their biological closeness to wildtype traits such as robustness, morphological or behavioural closeness to the aurochs.
Furthermore, the SNPs investigated are not a random sample, but likely based on SNP chips developed based on domestic cattle. SNP chips are assembled in a manner where domestic cattle are highly variable, otherwise they would be useless for the process. But the reconstructed aurochs genome is not that of a domestic individual but potentially a rather different, extinct genome. This problem is well-known and is called ascertainment bias [48]. If the SNP array covers regions of the genome where cattle breeds are highly polymorphic, which is to be assumed, it could be the case that aurochs variants that are rare or absent in domestic cattle are not covered. Regions where cattle are not highly variable, because domestic mutations might be fixed, usually do not get chosen for assembling an SNP array. But those are key regions when determining if a cattle breed is biologically closer to the aurochs or not. This skews the results even further.
Thus, it is not surprising that there is no correlation in Rewilding Europe’s Nei distance chart between scoring high and being less-derived (f.e. Simmental scoring higher than the Spanish fighting bull). A Nei distance chart of 700k SNPs using one aurochs genome as reference is simply not the appropriate method to determine which cattle breeds are close to the aurochs, if there is any noticeable difference among modern breeds in this regard at all. I suspect this is the reason why the Nei distance chart was not published in a technical paper but merely in a PDF by the organization.
Without having genes identified that played a key role during domestication and that are responsible for why cattle are cattle and not wild aurochs, we can hardly make any assumptions on which cattle populations are closer to the aurochs than others in a meaningful sense.
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