The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

Abstract

Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.

Alternate abstract:

eLife digest

For over five thousand years, domesticated cows and oxen in the Iberian Peninsula lived alongside their wild counterparts, the aurochs. These large and aggressive animals, from which modern European cattle descends, only went extinct during the 17^th century. Genetic evidence points to aurochs and livestock having interbred during their long coexistence; when and how these mixing events took place, however, remains unclear. Details regarding the management of ancient herds are also missing.

To address these questions, Günther et al. analysed the DNA extracted from ancient bovine bones sampled at four Iberic archaeological sites. This revealed that wild aurochs and cattle frequently interbred during the last 8,000 years. Mating principally took place between male aurochs and domesticated cows but slowed down after 4,000 years, resulting in modern cattle having inherited about 20% of genes from their wild relatives. This percentage was consistent across various breeds, including one renowned for its aggressivity and which has been selected for centuries for Spanish bullfighting.

Additional bone analyses revealed that aurochs and ancient cattle shared comparable diets composed primarily of wild vegetation. Only some domestic animals showed signs of having been fed crops.

These findings help us understand how modern cattle breeds came to be. The genes they inherited from aurochs may help them survive harsh environmental conditions, such as extreme heat or diseases. In the future, researchers could use this knowledge to refine breeding programs.

Introduction

Domestication of livestock and crops has been the dominant and most enduring innovation of the transition from a hunter-gathering lifestyle to farming societies. It represents the direct exploitation of genetic diversity of wild plants and animals for human benefit. Ancient DNA (aDNA) has proved crucial to understanding the domestication process and the interaction between domesticated species and their wild relatives both within domestication centres and throughout the regions that the domestics expanded into (Frantz et al., 2019; Frantz et al., 2020; Botigué et al., 2017; Irving-Pease et al., 2018; Verdugo et al., 2019; Daly et al., 2018; Daly et al., 2021; Fages et al., 2019; Librado et al., 2021; Yurtman et al., 2021; Bergström et al., 2020; Ginja et al., 2023; Larsson et al., 2024; Kaptan et al., 2024). The origins of the European domestic taurine, Bos taurus, are located in the Fertile Crescent (Peters et al., 1999; Helmer et al., 2005) and unlike dogs, pigs, and goats, where the wild forms are still extant, the wild cow (the aurochs) went extinct in 1627. Aurochs, Bos primigenius, was present throughout much of Eurasia and Africa before the expansion of domestic cattle from the Levant that accompanied the first farmers during the Neolithisation of Europe. Upon arrival, these early incoming domesticates inevitably coexisted with their wild counterparts in great parts of Europe facilitating gene flow in both directions. In general, taxa within the genus Bos can hybridise and produce fertile offspring (Zhang et al., 2020) which may have facilitated and contributed to domestication, local adaptation, and even speciation (Verdugo et al., 2019; Palacio et al., 2017; Wecek et al., 2017; Ward et al., 2022). Mitochondrial DNA studies have previously indicated gene flow between domestic cattle and aurochs outside their domestication centre (Beja-Pereira et al., 2006; Achilli et al., 2008; Schibler et al., 2014; Cubric-Curik et al., 2022; Bro-Jørgensen et al., 2018) and more recently, genomic studies have shown the presence of European aurochs ancestry in modern taurine cattle breeds (Park et al., 2015; Upadhyay et al., 2017; Rossi et al., 2024). Although cattle have represented a significant economic resource and a prominent cultural icon for millennia, and have been studied through aDNA for more than a decade (Verdugo et al., 2019; Beja-Pereira et al., 2006; Achilli et al., 2008; Park et al., 2015; Rossi et al., 2024; Anderung et al., 2005; Erven et al., 2024), our understanding of the interaction of early cattle herds and wild aurochs is still limited due to a lack of time-series genomic data. This gap of knowledge includes European aurochs’ genetic contribution to modern domestic breeds and human management of these animals in the past.

Aurochs have been widely exploited by humans since the European Palaeolithic and archaeological evidence indicates that the species survived in Europe until historical times. Iberia could have served as a glacial refugium for aurochs (Rossi et al., 2024), and the most recent evidence for aurochs is found at a Roman site in the Basque Country (Altuna, 2002). Domestic cattle were introduced into Iberia with the Mediterranean Neolithic expansion and reached the northern coast of the peninsula around 7000 years cal BP (Cubas et al., 2016). Consequently, aurochs and domestic cattle have coexisted in Iberia for about five millennia. Since then, cattle have played an important role in Iberian societies as a source of food and labour, as well as cultural events such as bullfighting. Currently, there are more than 50 bovine breeds officially recognised in the Iberian Peninsula including the Lidia breed, a primitive, isolated population selected for centuries to develop agonistic-aggressive responses with the exclusive purpose of taking part in such socio-cultural events (Cañón et al., 2008). Recently, it has been reported that Lidia breed individuals have the largest brain size among a comprehensive dataset of European domestic cattle breeds and are the most similar to wild aurochs (Balcarcel et al., 2021). The combination of aggressiveness and larger brain size in the Lidia breed may suggest a higher proportion of aurochs ancestry compared to other cattle breeds.

Here, we present the genomes and stable isotope data of Iberian Bovine specimens ranging from the Mesolithic into Roman times from four archaeological sites (Figure 1A). We explore the extent of interbreeding between wild aurochs and domestic cattle over time and the correlation of genetic ancestry with metric identification and ecological niches. Finally, we compare the results to genomic data obtained from modern Iberian cattle breeds to estimate the genetic contribution of the now-extinct aurochs to the Iberian farming economy.

Figure 1.

Data overview and descriptive ancestry analysis.

(A) Map of Europe showing the Iberian sampling sites (red circles, size proportional to sample sizes) and the sites for published aurochs genomes used in the analysis (blue diamonds). (B) Non-metric multi-dimensional scaling (NMDS) ordination of nuclear data of Iberian samples considered B. taurus samples (orange), Iberian samples that were morphologically considered B. primigenius (red), other Iberian Bos samples (brown), ancient domestic cattle from the Balkans and Anatolia (yellow), and aurochs (blue). Data point shape corresponds to mitochondrial haplogroups. (C) f₄ statistic measuring allele sharing of the Iberian samples with European aurochs (Bed3) or Anatolian Neolithic cattle (Sub1). Error bars indicate 95% confidence intervals estimated using a block jackknife procedure. The time periods displayed are contextual.

Results

Exploratory analysis

We successfully sequenced 24 bovine specimens excavated at four prehistoric sites in Iberia (Figure 1A). Nine of these individuals were inferred to or suspected to represent aurochs based on morphology or chronology. Direct radiocarbon dates and contextual dating placed the individuals between the Mesolithic (oldest sample moo001, 8641–8450 cal BP) and the Roman Age (youngest sample moo010p, 2260–2150 cal BP). It should be noted that while all post-Mesolithic samples were found at archaeological sites with evidence for herding of other domestic fauna such as ovicaprids (Appendix 1), we do not know whether these bovids were herded or hunted. Based on the number of reads mapping to the X chromosome, 13 individuals were identified as female and 11 as male, for the samples with sufficient amounts of reads for this analysis. Sequencing coverage of the nuclear cattle genome was low to medium, reaching up to 4.7× with a mean of 0.38× (Supplementary file 1). The sequence data for non-UDG-treated libraries showed damage patterns characteristic of aDNA (Appendix 2—figures 1–3). Based on reads mapping to the mitochondrial genome, we were able to estimate contamination for 11 samples with most samples showing low levels (<2%) of contamination. One individual (moo013a) showed a high contamination of 51.7% [33.5, 69.9] and was excluded from further analysis. One Mesolithic individual (moo040) showed 8.3% [3.1, 13.5] contamination, which was included in the initial exploratory analysis but not used for the analysis of hybridisation between wild and domestic as this analysis only focused on post-Mesolithic individuals.

Nine individuals were assigned to the mitochondrial P1 haplogroup, one to haplogroup T1, one to haplogroup T4, and 12 to haplogroup T3 (Supplementary file 1). P haplogroups are dominant among and thought to be endemic to European aurochs (Sinding and Gilbert, 2016), but are occurring at low frequencies in modern European cattle breeds (Cubric-Curik et al., 2022). The prevalence of the T3 haplogroup in our samples is expected; this haplogroup is dominant among modern European B. taurus and is the most common haplogroup in ancient Western European domestic cattle. T3 was found in directly dated Neolithic samples from different sites providing direct evidence for the arrival of domestic cattle in northern Iberia during the Neolithic (Supplementary file 1). The specimen assigned to T1 (moo009a) is notable since this individual was previously used to argue for Bronze Age contact between Iberia and Africa, where the T1 haplogroup is thought to have originated (Anderung et al., 2005; Colominas et al., 2015). T4 is usually considered to be restricted to Asian breeds with rare finds in Europe, restricted to the Balkans (Cubric-Curik et al., 2022). The presence of T4 in Chalcolithic Iberia suggests that this haplogroup must have been distributed across Western Europe at low frequencies in prehistory. Furthermore, the fact that some specimens that were morphologically identified as aurochs carry domestic T haplogroups implies some level of interbreeding between the two groups.

As mitochondrial genomes only reflect the maternal line of ancestry, they are not informative about the exact extent of interbreeding in our dataset. To avoid being constrained by the variation in modern domestic breeds as with common approaches such as projected principal component analysis (PCA) (Appendix 2—figure 4), we performed non-metric multi-dimensional scaling (NMDS) ordinations on a matrix of pairwise outgroup f₃ statistics to explore the genomic ancestry of the sequenced individuals. For reference, we included early cattle genomes from Anatolia and the Balkans as well as aurochs excavated from Morocco (Th7), Armenia (Gyu2), Anatolia (Ch22), Germany (Bed3), and Britain (CPC98) (Verdugo et al., 2019; Park et al., 2015; Erven et al., 2024), and calculated pairwise outgroup f₃ statistics. The NMDS ordination outcome (Figure 1B) seems to represent a separation between domestic autosomal ancestry (to the left) and European aurochs ancestry (to the right). In contrast, aurochs from other regions (Th7 and Gyu2) seem genetically distinct. Many early domestic samples from Iberia fall close to early cattle from the Balkans and Anatolia as well as the Anatolian aurochs (Ch22). Notably, at least two of the Iberian samples in this cluster (moo004, moo007) were morphologically identified as aurochs. Eight of the nine Iberian samples with haplogroup P fall to the right in the plot, together with the aurochs from Germany (Bed3) and Britain (CPC98). Additionally, one individual carrying a domestic T3 mitochondrial genome (moo019) appears closer to the aurochs samples than the domestics. Out of nine samples that were presumed aurochs based on their morphological features, only six would be considered aurochs based on this analysis. This highlights a substantial overlap between measurements or criteria that are used to distinguish wild and domestic Bos based on morphometrics.

This analysis suggests that one can use other European aurochs such as the German Bed3 (Bedburg-Königshoven, 11802–11326 cal BP) (Erven et al., 2024) or the British CPC98 (Carsington Pasture Cave, 6874–6602 cal BP) (Park et al., 2015) as a reference for Western European aurochs as they seem similar to our three low coverage Mesolithic Iberian samples. This is also supported by a recent parallel study concluding that all Western European aurochs form a clade, possibly even originating from an Iberian glacial refugium (Rossi et al., 2024). Using Sub1 (Suberde Höyük, 8171–7974 cal BP) (Verdugo et al., 2019), a Neolithic domestic Anatolian individual, and the higher coverage aurochs Bed3 as references, we can perform f₄ statistics to measure which Iberian individuals share more alleles with one or the other (Figure 1C). Despite the relatively low coverage of some samples, the f₄ statistics are highly correlated with the first axis of the NMDS (R²=0.84, p=8.3×10^–10) implying that they detect the same pattern. Non-overlapping confidence intervals also confirm that the high genetic differentiation between Western European aurochs and domestic cattle allows confident assignment even with low coverage data. The three Mesolithic individuals as well as an additional six, up until the Late Neolithic/Chalcolithic, share most of their alleles with aurochs. Three individuals from the Neolithic and Late Neolithic/Chalcolithic share most of their alleles with domestic Anatolian cattle while two individuals (moo012a and moo039) are more intermediate, suggesting that there could have been some level of hybridisation. More recent samples from the Bell Beaker period onwards all appear to have similar amounts of allele sharing with mostly domestic ancestry but some level of aurochs introgression.

Quantifying the extent of introgression

While f₄ statistics measure allele sharing it does not directly quantify the amount of introgression in the different specimens, hence, we employed three different frameworks to estimate ancestry proportions: f₄ ratio (Patterson et al., 2012), qpAdm (Haak et al., 2015; Harney et al., 2021), and Struct-f4 (Librado and Orlando, 2022) to model each Iberian individual from European aurochs (Bed3) and/or Anatolian Neolithic cattle (Sub1) as sources (Table 1). While the f₄ ratio provides a straightforward-to-interpret estimate of aurochs ancestry under a simple two-source model, we also include qpAdm due to the potential of rejecting models and hinting at additional ancestries. We also include Struct-f4 for better samples (>0.1×) as it is more flexible than qpAdm not requiring a strict separation between sources and outgroup populations. While quantitative estimates of European aurochs ancestry for the 20 post-Mesolithic individuals are somewhat correlated between f₄ ratio and qpAdm (Spearman’s correlation coefficient rho = 0.57, p=0.01), they differ for certain individuals. This highlights differences between the methods, their assumptions about the relationships of sources and outgroups, and their sensitivity to low coverage data. For most parts of this study, we decide to present the f₄ ratio results but it is important to highlight that our interpretations are based on the general pattern and not on the ancestry estimates for single individuals.

Table 1.

European aurochs ancestry proportions in post-Mesolithic Iberian Bos samples.

Square brackets are showing block-jackknife estimates of the 95% confidence interval. f₄ ratio and qpAdm are using Bed3 as source of European aurochs ancestry unless noted otherwise. Footnotes are added when deviations from the two-source model were needed. Struct-f4 was run in semi-supervised mode to estimate ancestry in the Iberian samples with K=5 as the different ancestries separated at this point. Only individuals with at least 0.1× coverage were included in this analysis to ensure convergence. LNCA = Late Neolithic/Chalcolithic.

Sample ID	Site	Period	Date cal BP	f4 ratio	qpAdm	Struct-f4 (K=5)
moo012a	El Portalón	Early Neolithic	contextual	0.908 [0.743, 1.072]	0.928 [0.77, 1.085]	–
moo004	Els Trocs	Neolithic	7152–6890	0.103 [0.025, 0.182]	0.06 [0.026, 0.098]*	0.01¶
moo007	Els Trocs	Neolithic	7151–6890	–0.089 [-0.204, 0.026]	0.073 [0.033, 0.113]*	0.039¶
moo014	El Portalón	Neolithic	6491–6403	0.861 [0.791, 0.931]	0.942 [0.905, 0.979]†	0.942¶
moo039	Mendandia	Neolithic	7426–7280	0.435 [0.334, 0.536]	0.866 [0.76, 0.971]	–
moo015	El Portalón	LNCA	5041–4842	–0.055 [-0.182, 0.072]	0.444 [0.32, 0.565]	–
moo017	El Portalón	LNCA	5567–5326	0.756 [0.646, 0.866]	0.811 [0.769, 0.853]*	–
moo019	El Portalón	LNCA	5556–5325	0.723 [0.628, 0.818]	0.828 [0.786, 0.87]*	0.654
moo020	El Portalón	LNCA	contextual	0.775 [0.652, 0.897]	0.944 [0.80, 1.085]	–
moo050	El Portalón	LNCA	5468–5320	0.788 [0.709, 0.866]	0.809 [0.773, 0.845]*	0.663**
moo011b	El Portalón	Bell Beaker	contextual	0.109 [-0.097, 0.316]	0.667 [0.47, 0.865]	–
moo012b	El Portalón	Bell Beaker	4421–4291	0.706 [0.528, 0.883]	0.326 [0.258, 0.394]*	–
moo022	El Portalón	Bell Beaker	contextual	0.169 [0.006, 0.332]	0.729 [0.55, 0.910]	–
moo023	El Portalón	Bell Beaker	4153–3976	0.179 [0.073, 0.285]	0.641 [0.54, 0.738]	0.21¶
moo033	El Portalón	Early Bronze Age	contextual	0.241 [0.050, 0.432]	0.987 [0.79, 1.182]	–
moo009a	El Portalón	Bronze Age	3884–3635	0.399 [0.297, 0.502]	0.284 [0.244, 0.324]*	0.152¶
moo009x	El Portalón	Bronze Age	3829–3513	0.198 [0.115, 0.280]	0.259 [0.203, 0.315]‡	0.176¶
moo034	El Portalón	Bronze Age	3811–3492	0.547 [0.300, 0.794]	0.112 [-0.061, 0.285]§	–
moo035	El Portalón	Bronze Age	contextual	0.307 [0.170, 0.445]	0.821 [0.68, 0.963]	–
moo010p	El Portalón	Roman	2334–2156	0.397 [0.205, 0.589]	0.281 [0.217, 0.345]*	–

*

To produce a fitting and feasible model (p>0.01) a minor contribution (≤ 5%) of indicine ancestry is required to fit the data.

†

Model does not fit with Bed3 as European aurochs source but fits well (p=0.49) when using CPC98.

‡

To produce a fitting and feasible model (p>0.01) a contribution of 33.7% Caucasus aurochs ancestry (Gyu2) is required to fit the data. This additional source is not well resolved as the standard error is large (21.2%).

§

To produce a fitting and feasible model (p>0.01) a contribution of 85.9% Caucasus aurochs ancestry (Gyu2) is required to fit the data. This additional source is not well resolved as the standard error is large (74.6%).

¶

Struct-f4 also assigns a small proportion of Caucasus aurochs ancestry (Gyu2) to this individual (<5%).

**

Struct-f4 also assigns a proportion of Caucasus aurochs ancestry (Gyu2) to this individual (14.0%).

Most of the 20 post-Mesolithic individuals show indications of both domestic and European aurochs ancestries (Table 1). Only three individuals (f₄ ratio) or one individual (qpAdm) do not show significant proportions of aurochs ancestry while only one individual (f₄ ratio) or three individuals show not significant proportions of domestic ancestry. Furthermore, qpAdm and Struct-f4 suggest low proportions of additional, eastern ancestries represented either by indicine cattle or the Caucasus aurochs Gyu2 in these analyses. While these ancestries are not well resolved and usually have high standard errors, they suggest that multiple western Asian populations contributed to the European early domestic gene pool. Notably, most Neolithic and pre-Bell Beaker Chalcolithic individuals show either predominantly domestic or aurochs ancestry while many Bell Beaker and Bronze Age individuals show more intermediate values of aurochs ancestry. In fact, from the Bronze Age onwards, most estimates overlap with the approximately 25% aurochs ancestry in modern Iberian cattle (Figure 2; Appendix 2—table 1; Eusebi et al., 2022).

Figure 2.

Development of aurochs ancestry over time.

Estimates of aurochs ancestry (estimated using the f₄ ratio with Bed3 as European aurochs source) in directly dated post-Mesolithic Iberian samples over time. Error bars indicate the 95% confidence interval estimated using a block-jackknife procedure. Modern Iberian whole-genome sequenced Lidia individuals are added around date 0 with some horizontal jitter. Approximate boundaries for the main sampling periods are indicated by dashed vertical lines.

A limitation of this analysis is the availability of genomes that can be used as representatives of the source populations. We used German and British aurochs to represent Western European aurochs ancestry and a single Anatolian Neolithic to represent the original domestic cattle that was introduced into Europe. Our Mesolithic Iberian aurochs contained too little endogenous DNA to be used as a proxy aurochs reference and all Neolithic and Chalcolithic samples estimated with predominantly aurochs ancestry (including the 2.7× genome of moo014) already carry low (but significant) levels of domestic ancestry. However, the fact that all of these aurochs samples carried P mitochondria strongly suggests that Western European aurochs can be considered monophyletic. Furthermore, a recent parallel study also concluded that all Western European aurochs form a clade (Rossi et al., 2024). The Anatolian Sub1 might also not be depleted of any European aurochs ancestry and could not fully represent the original European Neolithic gene pool as also indicated by qpAdm and Struct-f4 identifying small proportions of other Asian ancestries in some Iberian individuals. While these caveats should affect our quantitative estimates of European aurochs ancestry, they should not drive the qualitative pattern as our tests would still detect any excess European aurochs ancestry that was not present in Neolithic Anatolia.

An important question that remains unexamined is the exact process that led to the hybridisation since this could provide insight into human management practices or, more generally speaking, mating patterns between wild and domestic individuals. The fact that some individuals with predominantly aurochs ancestry carry T haplogroups (moo019) and that some individuals with predominantly domestic ancestry carry P haplogroups (moo009x) implies that females contributed in both directions. To assess whether the admixture process was sex-biased, we compared aurochs ancestry patterns on the X chromosome and autosomes (Figure 3). Since females carry two X chromosomes and males only have one, we can assume that an excess of a certain ancestry on the X chromosome indicates more females from that particular source population. While the estimates are noisy due to the low coverage data and even less sites available for the X chromosome, it is striking that all but one individual with mostly domestic autosomal ancestry (>50%) show even lower point estimates of aurochs ancestry on the X chromosome. This pattern even extends into the modern Iberian individuals. Male-biased aurochs introgression has been suggested based on mitochondrial haplotypes before (Verdugo et al., 2019). In the absence of aurochs Y chromosomal data, however, it is difficult to assess sex-biased processes from uniparental data alone. The comparison of X chromosomes and autosomes should theoretically have more power to detect such processes as they are less sensitive to genetic drift due to their recombining nature (Keinan et al., 2009) but estimation of ancestry proportions on the X chromosome can be affected by different biases (Lazaridis and Reich, 2017; Goldberg et al., 2017; Pfennig and Lachance, 2023). Overall, our results are consistent with previous observations that the contribution of wild ancestry into domestic cattle was mostly through aurochs bulls.

Figure 3.

Comparison of f₄ ratio estimated aurochs ancestry of post-Mesolithic Iberian samples on the autosomes vs X chromosomes.

Error bars indicate the 95% confidence interval estimated using a block jackknife procedure.

Aurochs ancestry in modern breeds and the Spanish Lidia cattle breed

We estimated aurochs ancestry in a set of Western European cattle breeds (Upadhyay et al., 2017) as we performed for the prehistoric samples. Previous studies have used D statistics for pairwise comparisons between breeds (Park et al., 2015; Upadhyay et al., 2017; da Fonseca et al., 2019). Such D statistics, however, are sensitive to biases including gene flow from populations not included in the analysis (Rogers and Bohlender, 2015). Furthermore, qpAdm provides the possibility to reject scenarios not fitting the data. Our point estimates for the aurochs ancestry range between 20% and 30% across all breeds (Figure 4) and do not show an increase in aurochs ancestry in Iberian breeds (da Fonseca et al., 2019). This result differs from the previous studies which suggested geographic differences in Western and Central Europe and we believe this could be due to ancestry from other, non-European groups in some commercial breeds (Appendix 2). Importantly, not all tested breeds did fit the simple two-source model Anatolian Neolithic domestic+European aurochs, likely representing low levels of contributions from other groups, e.g., indicine cattle (Upadhyay et al., 2017). The presence of indicine ancestry can be confirmed in a qpAdm analysis using three sources resulting in fitting models for all breeds (Appendix 2—table 4).

Figure 4.

qpAdm estimates of aurochs ancestry in modern Western European cattle breeds from the Upadhyay et al., 2017, dataset.

Commercial breeds are marked with a ‘C’. The figure is only showing breeds with feasible and non-rejected two-source models, as all results are shown in Appendix 2—table 1. Error bars are showing block-jackknife estimates of the 95% confidence interval.

Figure 4—figure supplement 1.

qpAdm aurochs ancestry estimates for the six individual Lidia genomes.

Cattle have played an important role in Iberian culture during the last centuries as they have been part of numerous traditional popular events including bullfighting. The Lidia breed, a heterogeneous group of Iberian cattle that is mainly bred for aggressive behaviour, has commonly been used for such popular festivities (Cañón et al., 2008). Even though Lidia cattle has only been actively bred for agonistic behaviour for about 200 years, some people attribute their aggressiveness and appearance as an indication of high levels of aurochs ancestry (Balcarcel et al., 2021). We additionally use medium coverage genomes of six Lidia individuals (Eusebi et al., 2022) to estimate their proportion of aurochs ancestry. Lidia cattle in the Upadhyay et al., 2017, dataset had a point estimate of 25% (95% confidence interval: [18.5, 31.5]) aurochs ancestry and estimates in the individual genomes ranged from 17.6% [10.9, 24.3] to 23.5% [17.0, 30.0] (Figure 4—figure supplement 1) – all overlapping with the observed range for other Western European breeds. Despite some variation between individuals, which might be attributable to noise due to low coverage sequencing data in the reference populations, we do not observe a systematically elevated level of aurochs ancestry compared to other modern breeds or ancient samples since the Bronze Age. While these results reject the idea that the specifics of Lidia cattle can be attributed to a substantially increased genome-wide aurochs ancestry, it does not rule out the possibility that the roots of their aggressiveness and appearance are indeed due to aurochs variants at key loci responsible for those traits. An in-depth investigation of such questions would require a larger dataset of aurochs genomes as well as a more comprehensive Lidia sampling due to their fragmentation in highly distant genetic lineages (Cañón et al., 2008).

Stable isotope analysis

In addition to their ancestry, we studied the ecology of the bovids through stable isotope analysis of bone collagen. Lynch et al., 2008, suggested that stable isotope data could be used to infer niche separation between the species in Britain, with domestic cattle in more open settings, while aurochs (about 1‰ more depleted in δ¹³C) were habitually in more forested areas, or wet ground. This is most likely facilitated through human management of the domestic cattle, separating them from their wild counterparts. In contrast, Noe-Nygaard et al., 2005, failed to observe such an effect in samples from Denmark and northern Germany.

Considering our dataset and other data published on Iberian cattle (categorised on morphology/date) (Fernández-Crespo and Schulting, 2017; Fontanals-Coll et al., 2015; Garcia Guixé et al., 2006; Jones et al., 2019; Navarrete et al., 2017; Salazar-García, 2009; Salazar-García, 2011; Salazar-García et al., 2014; Sarasketa-Gartzia et al., 2018; Villalba-Mouco et al., 2018), we observe that the nitrogen isotope means are statistically different only when our data are compared using morphological characteristics, not genetic distinctions (see Supplementary file 1 and Appendix 3). This difference is mostly due to some domestic cattle with δ¹⁵N values greater than 6.5‰. This could be explained by some taurine cattle having exclusive habitual access to high nitrogen isotope ratio resources. For example, human management such as corralling on manured ground, or feeding with manured crops, would produce this effect. Nevertheless, there is generally a large amount of overlap in the isotope values for the two groups suggesting that wild and domesticated groups often did not occupy different niches in Iberia.

Discussion

We generated and analysed biomolecular data from B. primigenius and B. taurus spanning more than 9000 years in the same region. Cattle are important livestock in the Iberian Peninsula today, and our results illustrate the interaction between domestic cattle and their wild relatives in the past. The two groups show signs of frequent hybridisation starting soon after the arrival of cattle to the peninsula, as evident in our oldest directly dated Neolithic individual (moo039, 7426–7280 cal BP) where signals of carrying both ancestries are clear. Throughout the Neolithic, we observed large variations in the wild vs domestic ancestry per individual, but this pattern later stabilised (to 20–30% aurochs ancestry) from the Chalcolithic/Bronze Age onwards. As we do not know whether the sequenced individuals were hunted or herded, this could reflect a transition from hunting and herding to predominantly herding and it is possible that systematic herd management led to the nearly constant levels of aurochs ancestry over the last 4000 years. This period also coincides with several other societal changes; including the Bell Beaker complex and the introduction of human ancestry from the Pontic steppe into the Iberian Peninsula (Olalde et al., 2018; Valdiosera et al., 2018; Olalde et al., 2019). Around this time, humans also started processing a significantly higher amount of dairy products connected with the ‘secondary product revolution’ (Francés-Negro et al., 2021; Evershed et al., 2022). Aurochs were probably present in Iberia until Roman times (Altuna, 2002) leaving possibilities for interbreeding but we cannot exclude that various factors such as hunting or changing vegetation had led to a substantial decline in the wild aurochs population around the early Bronze Age. A previous study on cattle morphology from the site of El Portalón described a decrease in size from the Neolithic to the Chalcolithic and a further significant size decrease from the Chalcolithic to the Bronze Age (Galindo-Pellicena et al., 2020) and associated this change in size to the aridification of the area at this time (Martínez-Pillado et al., 2014). Indeed, this climatic change could also be related to a reduction of the aurochs population contributing to the stabilisation of the levels of ancestry in domestic cattle from the Bronze Age to the present. Nonetheless, our stable isotope results suggest that wild and domesticated groups often did not occupy substantially different niches on the Iberian Peninsula. Material excavated from Denmark suggested that aurochs changed their niches over time (Noe-Nygaard et al., 2005) demonstrating some flexibility depending on local vegetation and the possibility of aurochs adapting to changing environments.

The reduced level of aurochs ancestry on the X chromosome (compared to the autosomes) in admixed individuals suggests that it was mostly aurochs males who contributed wild ancestry to domestic herds, a process that had been suggested based on the distribution of mitochondrial haplotypes before (Verdugo et al., 2019). A recent parallel study based using ancient genomes also detected male-biased aurochs introgression using similar methods as our study (Rossi et al., 2024). Consequently, the offspring of wild bulls and domestic cows could be born into and integrated within managed herds. It is unclear how much of this process was intentional but the possibility of a wild bull inseminating a domestic cow without becoming part of the herd suggests that some level of incidental interbreeding was possible. For Neolithic Turkey, it has been suggested that allowing insemination of domesticated females by wild bulls was intentional, maybe even ritual (Peters et al., 2012). Modern breeders are still mostly exchanging bulls or sperm to improve their stock which manifests in a lower between-breed differentiation on the X chromosome (da Fonseca et al., 2019).

The lack of correlation between genomic, stable isotope, and morphological data highlights the difficulties of identifying and defining aurochs to the exclusion of domestic cattle. All of these data measure different aspects of an individual: their ancestry, ecology, or appearance, respectively. While they can give some indication, none of them are a direct measurement of how these cattle were recognised by prehistoric humans or whether they were herded or hunted. It remains unclear whether our ancestry inferences had any correlation to how prehistoric herds were managed and how much intentional breeding is behind the observed pattern of hybridisation. It is even possible that all hybrids identified in this study were part of domestic herds.

Even though wild aurochs populations went extinct, European aurochs ancestry survived into modern cattle with a relatively uniform distribution across Western European breeds. Isolated Iberian Lidia, bred for their aggressiveness, appears to be no exception to this pattern. This rejects the notion that an overall increased proportion of aurochs ancestry causes the distinctiveness of certain breeds, but considering the functional relevance of archaic introgression into modern humans (Reilly et al., 2022), it is possible that aurochs variants at functional loci may have a substantial influence on the characteristics of modern cattle breeds. Our low coverage sequencing data did not allow us to investigate this but future bioarchaeological studies combining different types of data will have the possibility to clarify the role of the extinct aurochs ancestry in modern domestic cattle.

Conclusions

Using a bioarchaeological approach we have demonstrated that since cattle arrived in Iberia there has been hybridisation with the local aurochs population, and that mainly aurochs bulls contributed to the gene pool still found in domestic herds today. Admixture proportions vary for the first few millennia but stabilise during the Bronze Age at approximately 20–30% of wild ancestry in the individuals found at the Iberian archaeological sites, a level that is still observed in modern Iberian breeds, including the more aggressive Lidia breed. This development could be the result of an initial mix of hunting and herding together with a generally loose management of herds, becoming more controlled over time in combination with a reduced importance of hunting wild aurochs.

The amount of hybridisation observed in the ancient cattle makes it difficult to genetically define what a domestic or wild Bos is, bringing into doubt the validity of such categorisations. Our interpretation is made more difficult by the overlap in morphological and metric data, creating further difficulties in species determination (especially in hybrids) and niche sharing as revealed by stable isotopes. To some extent, our interpretation is moot, as the salient matter is, how did prehistoric humans interact with cattle? What was their sense of wild and domestic and hybridisation? While we have recognised individual hybrids, to what extent these were part of domestic herds or intentionally bred and managed is uncertain.

Another source of uncertainty in our determinations is the limited knowledge about the genetic diversity in European aurochs. Further regional (and temporally longitudinal) aurochs genomes would aid future genomic studies defining the genetic variation in the European aurochs population.

Materials and methods

Data generation

We attempted DNA extractions of 50 archaeological remains from which we successfully extracted DNA from 24 individuals identified as domestic cattle and aurochs excavated from four prehistoric sites in Iberia: El Portalón de Cueva Mayor (n=18), Artusia (n=1), Els Trocs (n=2), and Mendandia (n=3). Teeth and bones were UV irradiated (6 J/cm² at 254 nm) and the first millimeter of bone/tooth surface abraded using a Dremel tool. DNA was extracted in a dedicated aDNA facility using a silica-based DNA extraction protocol (Dabney et al., 2013). For each sample, 100–200 mg of bone or tooth powder were incubated for 24 hr at 37°C, using the MinElute column Zymo extender assembly replaced by the High Pure Extender Assembly (Roche High Pure Viral Nucleic Acid Large Vol. Kit) and performed twice for each sample. DNA extracts were subjected to UDG treatment for the removal of deaminated cytosines and were further converted into blunt-end double-stranded Illumina multiplex sequencing libraries (Meyer and Kircher, 2010). Between seven and fifteen qPCR cycles were performed to amplify the DNA libraries using indexed primers (Meyer and Kircher, 2010). These were subsequently pooled at equimolar concentrations and shotgun sequenced on Illumina HiSeq and NovaSeq sequencing platforms.

Radiocarbon dates

Eight bone and teeth were directly radiocarbon dated (AMS) at Waikato University in New Zealand and two teeth at Beta Analytics in the United States. Radiocarbon dates were calibrated using the OXcal 4.4 program (Bronk Ramsey, 2009) and the IntCal20 calibration curve (Reimer et al., 2020). Three samples from the site of Mendandia were conventionally radiocarbon dated at Groningen (Netherlands) radiocarbon laboratory and calibrated as above.

Stable isotopes analysis

Many of the samples analysed here were radiocarbon dated and stable isotope data (via IRMS) were generated in this process, to augment this data we also produced stable isotope data for some additional samples in this dataset, where they were available. The additional samples underwent bone collagen or tooth dentine collagen extraction at the Laboratorio de Evolución Humana (Universidad de Burgos) following the protocol of Richards and Hedges, 1999. In brief, this is a cold acid demineralisation, followed by Milli-Q water rinsing, gelatinisation at pH 3 (24 hr at 70°C), Ezee filtering, and lyophilisation. Collagen yields (as % mass of starting bone) were recorded. Stable isotope values (δ¹³C, δ¹⁵N) and %C, %N were measured in duplicate at the Universitat Autònoma de Barcelona, unless only one sample was successful in the analysis. Collagen samples (approx. 0.4 mg) were analysed using a Flash IRMS elemental analyser coupled to a Delta V Advantage isotope ratio mass spectrometer (IRMS), both from Thermo Scientific (Bremen, Germany) at the Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona (ICTA-UAB). International laboratory standard IAEA-600 was used, with measurements made relative to Vienna PeeDee Belemnite (V-PDB) for δ¹³C, and air N₂ (AIR) for δ¹⁵N. The average analytical error was <0.2‰ (1σ) as determined from the duplicate analyses of δ¹³C and δ¹⁵N. In-house standards used was dog hair collected and homogenised for interlaboratory comparisons.

Data processing

HiSeq X10 reads have been trimmed and merged using AdapterRemoval (Schubert et al., 2016) while adapters for NovaSeq 6000 reads have been trimmed with cutadapt (Martin, 2011) and merging was performed with FLASH (Magoč and Salzberg, 2011) requiring a minimum overlap of 11 bp. Single-end reads of at least 35 bp length were then mapped to the cattle reference genomes UMD3.1 (Zimin et al., 2009) and Btau5 (Cattle Genome Sequencing International Consortium, 2015) using bwa (Li and Durbin, 2009) with the non-default parameters: -l 16500, -n 0.01, and -o 2. Different sequencing runs per sample were merged with samtools (Li et al., 2009) and consensus sequences were called for duplicate sequences with identical start and end coordinates (Kircher and Clifton, 2012). Finally, reads with more than 10% mismatches to the reference genome were removed. Biological sex was assigned to the samples mapped to the Btau_5 reference genome (as UMD3.1 does not contain a Y chromosome assembly) using the R_x method (Mittnik et al., 2016) modified for 29 autosomes.

Mitochondrial contamination was estimated following the approach used by Green et al., 2008, for hominins. We first identified nearly private mutations (less than 5% frequency in the 278 diverse mitogenomes used by MitoToolPy and dometree Peng et al., 2015, obtained from Dryad, https://doi.org/10.5061/dryad.cc5kn) in each individual and then used the proportion of non-consensus alleles at these sites to estimate contamination. We restricted this analysis to sites with at least 10× coverage, a minimum base quality of 30. Furthermore, transition sites with a C or G in the consensus mitogenome were excluded to avoid over-estimation due to post-mortem damage. Standard errors were estimated assuming a binomial distribution around the point estimate. Code used for this step can be found at https://github.com/GuntherLab/mt_contam_domestic_green, copy archived at Günther, 2024.

For comparative purposes, we also processed published data from Verdugo et al., 2019; Palacio et al., 2017; Wecek et al., 2017; Park et al., 2015, using the same bioinformatic pipeline. Furthermore, we downloaded sequence data for six Spanish Lidia cattle (Eusebi et al., 2022), a single modern water buffalo (Bubalus bubalis, Jaffrabadi-0845) (Dutta et al., 2020) and a single zebu cattle individual (Sha_3b) (Chen et al., 2018) and processed them with our aDNA mapping pipeline. To obtain a pseudohaploid Yak (Bos grunniens) sequence, we followed the approach by Upadhyay et al., 2017, splitting the Yak reference genome (Hu et al., 2012) contigs into 100 bp fragments and mapping them to the UMD3.1 reference genome.

Data analysis

Mitochondrial consensus sequences were called using ANGSD (Korneliussen et al., 2014) and the options -doFasta 2 -doCounts 1 -minQ 30 -minMapQ 30. Mitochondrial haplogroups were then assigned to the whole mitogenome sequences using the Python script MitoToolPy (Peng et al., 2015).

For population genomic analysis, we used a panel of SNPs derived from Run6 of the 1000 genomes project (Daetwyler et al., 2014; Hayes and Daetwyler, 2019). We obtained a list of SNPs from Naval-Sánchez et al., 2020, and reduced the panel to biallelic SNPs of at least 10% minor allele frequency in the joint European B. taurus/Asian Bos indicus dataset. Prior to genotype calling, all ancient BAM files were modified such that Ts in the first 5 bases of each fragment and As at the last 5 base pairs of each fragment have a base quality of 2. This approach allows to include more sites than excluding all transitions which are potentially affected by post-mortem damage. Prior to genotype calling, all ancient BAM files were modified such that Ts in the first 5 bases of each fragment and As at the last 5 base pairs of each fragment have a base quality of 2. As this is an approach that is not widely used, we compared its effect on downstream analysis. As our main analyses are all based on f statistics, we compared f₄ statistics (Figure 5) and f₄ ratios (Figure 6) of our rescaled base quality data with data only using transversion sites. While estimates are highly correlated, the dataset reduced to transversions produces larger confidence intervals in f₄ ratios due to the lower number of sites (Figure 6). Consequently, we decided to use the rescaled data for all analyses displayed in the main figures.

Figure 5.

f₄ statistics contrasting our newly sequenced samples to a reference domestic individual and a reference European aurochs.

The f₄ statistics were calculated for two different versions of the bam files: with rescaled bases in fragment ends vs untreated bam files but an SNP panel excluding transitions. The blue line indicates a linear regression with confidence interval. Error bars indicate 95% confidence intervals estimated using a block jackknife procedure.

Figure 6.

f₄ratios estimating European aurochs ancestry in our newly sequenced Iberian samples.

The f₄ ratios were calculated for two different versions of the bam files: with rescaled bases in fragment ends vs untreated bam files but an SNP panel excluding transitions. The right panel shows the standard errors for the f₄ ratio estimates, the dashed line would correspond to equal standard errors for the two panels. Error bars indicate 95% confidence intervals estimated using a block jackknife procedure.

To generate pseudohaploid representations of each individual, we randomly draw a single read with mapping and base quality of at least 30 at each SNP position. If the allele carried by the ancient individual was not one of the two known alleles, we removed the site from the panel. Using this approach, ~9.1 million autosomal and 248K X chromosomal SNPs were genotyped in the ancient samples. To compare the ancient samples to a diverse set of modern cattle, we used the panel of modern European breeds presented by Upadhyay et al., 2017, which were genotyped at ~770,000 SNPs. The ancient samples were genotyped the same way as for the 1000 Bulls project SNP panel.

To conduct an ordination of the nuclear data, sequences of 43 ancient Eurasian cattle and two aurochs were obtained from Park et al., 2015, and Verdugo et al., 2019. Outgroup f₃ statistics were calculated for all pairs of our Iberian Bos samples, using a Yak (B. grunniens) genome as an outgroup, and a distance matrix for all samples was calculated as 1 f₃. All f statistics were calculated in R version 4.1.2 (R Development Core Team, 2016) package ‘admixtools2’ (Maier et al., 2023). The distance matrix was used to compute scores for NMDS ordinations using the metaMDS function in the ‘vegan’ R package and 10,000 random starts (Oksanen et al., 2020).

European aurochs introgression α into Iberian individual X was estimated using f₄ ratios calculated with POPSTATS (Skoglund et al., 2015) and the equation$\alpha =1-\frac{f_4\left(Gyu2,YAK;X,EuropeanAurochs\right)}{f_4\left(Gyu2,YAK;Sub1,EuropeanAurochs\right)}$

Both Bed3 and CPC98 were separately tested as aurochs source and Bed3 was chosen for the results presented in the article due to lower confidence intervals. POPSTATS was run with the non-default options –ratio, –testpop, and –not23 to allow for more autosomes than humans have. We also used admixtools2 (Maier et al., 2023) and qpAdm (Haak et al., 2015; Harney et al., 2021) to model the ancestry proportions in the samples. Bed3 was used as a source for European aurochs ancestry (due to lower standard errors in the f₄ ratios) while the domestic Anatolian Neolithic Sub1 was used as a source for domesticated cattle ancestry. As ‘right’ populations, we used Gyu2, B. indicus, Yak and Bison bonasus bonasus PLANTA. qpAdm was run with auto_only = FALSE, maxmiss = 0.5 and allsnps = TRUE. When the two-source model did not fit (p<0.01) or produced infeasible admixture proportions outside [0, 1], we used rotate_models and qpadm_multi to find alternative models adding CPC98 as an additional possible source or ‘right’ population. qpAdm was also used for the modern Western European breed panel from Upadhyay et al., 2017, adding Bes2 (Verdugo et al., 2019) to the ‘right’ populations and excluding breeds from Italy and the Balkan from the targets as non-taurine ancestry (Upadhyay et al., 2017) in them would lead to a rejection of the models. Finally, we also used Struct-f4 (Librado and Orlando, 2022) to estimate ancestry proportions. First, input files were generated with the provided helper scripts and f₄ statistics were calculated in blocks of 5Mbp. Struct-f4 was then run in semi-supervised mode with default parameters to estimate ancestries in Iberian individuals with at least 0.1× coverage. This cutoff was chosen as lower coverage samples prevented conversion. CPC98, YAK, Ch22, Gyu2, Bed3, Sub1, and Sha_3b were used as additional individuals to provide a framework of different possible ancestries.

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