Early cattle management in NE China

From the paper:

The haplogroup retrieved has so far not been found in modern cattle. However, as mtDNA represents a single genetic locus, it is prone to genetic drift and could easily have been lost by drift even if hybridization between the population to which the Chinese specimen belonged and other domesticated cattle populations has occurred. Further analyses on nuclear DNA will be necessary to show whether this early Chinese cattle management was a short-lived episode or whether it has contributed to the nuclear gene pool of modern cattle.

Nature Communications 4, Article number: 2755 doi:10.1038/ncomms3755

Morphological and genetic evidence for early Holocene cattle management in northeastern China

Hucai Zhang et al.

The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent 14C dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.

Link

Ancestry and Admixture of Domesticated Cattle

Quite an interesting new preprint on the arXiv.

arXiv:1309.5118 [q-bio.PE]

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

Jared E. Decker et al.

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle are shown to be of Iberian, and not African, decent. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.

Link

Paternal origins of Chinese cattle

The taurine/indicine north/central vs. south China makes sense. Also of interest, the dominance (within the taurine group) of Y2 over Y1 haplogroup. I had wished for more eastern data points when Edwards et al. was published and it now appears clear that at least in the case of China there is a predominance of the Y2 (southern) haplogroup within the taurine group of patrilineages.

Anim Genet. 2013 Jan 24. doi: 10.1111/age.12022. [Epub ahead of print]

Paternal origins of Chinese cattle.

Li R, Zhang XM, Campana MG, Huang JP, Chang ZH, Qi XB, Shi H, Su B, Zhang RF, Lan XY, Chen H, Lei CZ.

logy, Northwest A&F University, Yangling, Shaanxi, 712100, China. Abstract

To determine the genetic diversity and paternal origin of Chinese cattle, 302 males from 16 Chinese native cattle breeds as well as 30 Holstein males and four Burma males as controls were analysed using four Y-SNPs and two Y-STRs. In Chinese bulls, the taurine Y1 and Y2 haplogroups and indicine Y3 haplogroup were detected in seven, 172 and 123 individuals respectively, and these frequencies varied among the Chinese cattle breeds examined. Y2 dominates in northern China (91.4%), and Y3 dominates in southern China (90.8%). Central China is an admixture zone, although Y2 predominates overall (72.0%). The geographical distributions of the Y2 and Y3 haplogroup frequencies revealed a pattern of male indicine introgression from south to north China. The three Y haplogroups were further classified into one Y1 haplotype, five Y2 haplotypes and one Y3 haplotype in Chinese native bulls. Due to the interplay between taurine and indicine types, Chinese cattle represent an extensive reservoir of genetic diversity. The Y haplotype distribution of Chinese cattle exhibited a clear geographical structure, which is consistent with mtDNA, historical and geographical information.

Link

Small number of founders of modern Taurine Cattle

Mol Biol Evol (2012) doi: 10.1093/molbev/mss092

Modern Taurine Cattle descended from small number of Near-Eastern founders

Ruth Bollongino et al.

Abstract

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challenging process. We report mitochondrial DNA sequences from 15 Neolithic to Iron Age Iranian domestic cattle and, in conjunction with modern data, use serial coalescent simulation and approximate Bayesian computation to estimate that around 80 female aurochs were initially domesticated. Such a low number is consistent with archaeological data indicating that initial domestication took place in a restricted area and suggests the process was constrained by the difficulty of sustained managing and breeding of the wild progenitors of domestic cattle.

Link

Frachetti on the multiregional emergence of mobile pastoralism

I had previously posted on horses not being important for the emergence of steppe pastoralism, in which Frachetti and Benecke documented how the early (4,500ky) Begash culture of Kazakhstan had developed full-blown pastoralism without apparently relying on horses.

This is in contradistinction to both the Botai culture where there is abundant evidence for horse use, apparently for food, as well as the Eneolithic cultures of the European steppe where horse bones are much more prevalent than in early Begash.

The simple model of the emergence of pastoral nomadism proposes the spread of this mode of subsistence from the European (Pontic-Caspian) steppe, together with horses and horse-drawn vehicles. Popularized by David Anthony in recent years, this model views horses and wheels as the great enablers of pastoralism, and views the emergence of pastoral cultures across the steppe as the result of movements of mobile pastoralists -atop their horses, and with their herds- across the Eurasian steppe.

Frachetti is a critic of this model, and proposes instead the importance of the (hitherto neglected) Inner Asian Mountain Corridor as important in facilitating prehistoric contacts between east and west. In a new paper in Current Anthropology he elaborates on his proposed "multiregional" model of the emergence of mobile pastoralism.

I have not read the paper's 38 pages carefully yet (including CA comments and response), but this is clearly a seminal work on the studied topic that will be referenced for years to come. I will post any specific comments in updates to this post. For the moment, I will limit myself to a couple of observations:

• Recent work in Y-chromosome phylogeny has established a fairly disjoint division within haplogroup R1a1a; in particular the R-Z93 subhaplogroup seems to abound in the "Asian steppe", as well as Asia in general, while being generally absent in Europe; the R1a1a and Subclades Y-DNA Project is keeping track of new developments in this field.
• My own research on autosomal DNA, suggests the confluence of two "streams" of ancestry onto the steppe: a west-to-east stream emanating from eastern Europe, and associated with the Atlantic_Baltic (K7b) or North_European (K12b) ancestral component; as well as a West_Asian (K7b) or Caucasus/Gedrosia (K12b) component emanating from the highland regions south of the Caspian and south of the steppe (the traditional Silk Road territory).

These lines of evidence certainly appear to be consistent with a "multiregional" model of early mobile pastoralism. In particular they testify to the non-uniformity of ancestry of steppe groups and are inconsistent with their derivation from a single source. The picture is further complicated by the historical movements of nomads across the steppe (including Scytho-Sarmatian type people as well as Turkic-Mongolian ones). Charting the emergence of steppe populations will require a great deal of sleuthing in the genomes of modern steppe inhabitants, as well as a great deal of work on ancient DNA.

In any case, the new paper by Michael Frachetti will provide important new insight to all those who seek to understand "what actually happened" in Eurasian prehistory, and it is a very welcome addition to the ongoing debate.

Current Anthropology Vol. 53, No. 1, February 2012

Multiregional Emergence of Mobile Pastoralism and Nonuniform Institutional Complexity across Eurasia

Michael D. Frachetti


Abstract

In this article I present a new archaeological synthesis concerning the earliest formation of mobile pastoralist economies across central Eurasia. I argue that Eurasian steppe pastoralism developed along distinct local trajectories in the western, central, and (south)eastern steppe, sparking the development of regional networks of interaction in the late fourth and third millennia BC. The “Inner Asian Mountain Corridor” exemplifies the relationship between such incipient regional networks and the process of economic change in the eastern steppe territory. The diverse regional innovations, technologies, and ideologies evident across Eurasia in the mid-third millennium BC are cast as the building blocks of a unique political economy shaped by “nonuniform” institutional alignments among steppe populations throughout the second millennium BC. This theoretical model illustrates how regional channels of interaction between distinct societies positioned Eurasian mobile pastoralists as key players in wide-scale institutional developments among traditionally conceived “core” civilizations while also enabling them to remain strategically independent and small-scale in terms of their own sociopolitical organization. The development of nonuniform institutional complexity among Eurasian pastoralists demonstrates a unique political and economic structure applicable to societies whose variable political and territorial scales are inconsistent with commonly understood evolutionary or corporate sociopolitical typologies such as chiefdoms, states, or empires.

Link

Short-legged Neandertal mystery solved (and other interesting thoughts)

A nice new paper proposes that Neandertal short legs were not due to adaptation to cold but related to gait efficiency in a mountainous environment. A short-legged person usually has to use more strides/time unit to keep up with a long-legged one. What the researchers have shown is that on a slope this is not the case.

An interesting thought came to me as I was reading this: if Neandertal short legs were not due to cold adaptation, could it be that early Homo sapiens long legs were also not due to adaptation for a tropical climate?

It has been generally believed that the longer legs of early Upper Paleolithic humans in Europe compared to Neandertals evidenced their fairly recent arrival from a much warmer region.

But, in an age when there was no alternative to walking, we would expect populations that migrated over long distances to be efficient walkers, or to become so, en route, due to natural selection ("those who can't keep up stayed behind"). Moreover, while all humans are pretty much capable of walking anywhere, we would expect the pioneers in every region colonized by our species to be longer-limbed, since they "got there first".

The reverse could also be true, depending on the environment one walked through: early colonists of mountainous regions might be rather short-legged, and this is exactly what we find in the "hyper-polar" body types of early Neolithic farmers. These had to move across the fairly uneven terrain of southeastern Europe, at an age when there were no maps, no roads, and plenty of forest, making the shortest path between two points something different than a horizontal line.

The press release explains things quite well:

While most studies have concluded that a cold climate led to the short lower legs typical of Neandertals, researchers at Johns Hopkins have found that lower leg lengths shorter than the typical modern human's let them move more efficiently over the mountainous terrain where they lived. The findings reveal a broader trend relating shorter lower leg length to mountainous environments that may help explain the limb proportions of many different animals.

...

"Studies looking at limb length have always concluded that a shorter limb, including in Neandertals, leads to less efficiency of movement, because they had to take more steps to go a given distance," says lead author Ryan Higgins, graduate student in the Johns Hopkins Center of Functional Anatomy and Evolution. "But the other studies only looked at flat land. Our study suggests that the Neandertals' steps were not less efficient than modern humans in the sloped, mountainous environment where they lived."

...

Neandertals, who lived from 40,000 to 200,000 years ago in Europe and Western Asia, mostly during very cold periods, had a smaller stature and shorter lower leg lengths than modern humans. Because mammals in cold areas tend to be more compact, with a smaller surface area, scientists have normally concluded that it was the region's temperature that led to their truncated limbs compared to those of modern humans, who lived in a warmer environment overall.

...

The researchers decided to study different types of bovids--a group of mammals including gazelles, antelopes, goats and sheep--since these animals live in warm and cold environments on both flat and hilly terrain. The group took data from the literature on bovid leg bones and found that they fit the pattern: mountainous bovids, such as sheep and mountain goats, overall had shorter lower leg bones than their relatives on flat land, such as antelopes and gazelles, even when they lived in the same climates.

Investigating closely related bovids brought this trend into even sharper relief. Most gazelles live on flat land, and the one mountainous gazelle species examined had relatively shorter lower legs, despite sharing the same climate. Also, among caprids (goats and sheep), which mostly live on mountains, the one flat land member of the group exhibited relatively longer lower legs than all the others.

"Biologists have Bergman's and Allen's Rules, which predict reduced surface area to body size and shorter limbs in colder environments," says Higgins. "Our evidence suggests that we can also predict certain limb configurations based on topography. We believe adding the topic of terrain to ongoing discussions about limb proportions will allows us to better refine our understanding of how living species adapt to their environments. This improved understanding will help us better interpret the characteristics of many fossil species, not just Neandertals."

Am J Phys Anthropol DOI: 10.1002/ajpa.21575

The effects of distal limb segment shortening on locomotor efficiency in sloped terrain: Implications for Neandertal locomotor behavior

Ryan W. Higgins, Christopher B. Ruff

Past studies of human locomotor efficiency focused on movement over flat surfaces and concluded that Neandertals were less efficient than modern humans due to a truncated limb morphology, which may have developed to aid thermoregulation in cold climates. However, it is not clear whether this potential locomotor disadvantage would also exist in nonflat terrain. This issue takes on added importance since Neandertals likely spent a significant proportion of their locomotor schedule on sloped, mountainous terrains in the Eurasian landscape. Here a model is developed that determines the relationship between lower limb segment lengths, terrain slope, excursion angle at the hip, and step length. The model is applied to Neandertal and modern human lower limb reconstructions. In addition, for a further independent test that also allows more climate-terrain cross comparisons, the same model is applied to bovids living in different terrains and climates. Results indicate that: (1) Neandertals, despite exhibiting shorter lower limbs, would have been able to use similar stride frequencies per speed as longer-limbed modern humans on sloped terrain, due to their lower crural indices; and (2) shortened distal limb segments are characteristic of bovids that inhabit more rugged terrains, regardless of climate. These results suggest that the shortened distal lower limb segments of Neandertals were not a locomotor disadvantage within more rugged environments.

Link

Of Cattle and Men (Edwards et al. 2010)

From the paper:

Apparently, the expansion of the dairy breeds have created, or largely maintained, a sharp genetic contrast of northern and southern Europe, which divides both France and Germany. It may be hypothesised that the northern landscapes, with large flat meadows, are suitable for large-scale farming with specialised dairy cattle (Niederungsvieh, lowland cattle), whilst the mixed-purpose or beef cattle (Höhenvieh, highland cattle) are better suited to the smaller farms and hilly regions of the south. However, it is also remarkable that in both France and Germany the bovine genetic boundary coincides with historic linguistic and cultural boundaries. In France, the Frankish invasion in the north created the difference between the northern langue d'oïl and the southern langue d'oc. The German language is still divided into the southern Hochdeutsch and northern Niederdeutsch dialects, which also correlates with the distribution of the Catholic and Protestant religions. On a larger scale, it is tempting to speculate that the difference between two types of European cattle reflects, and has even reinforced, the traditional and still visible contrast of Roman and Germanic Europe.

UPDATE: I wish there'd be some data points for the vast area between Eastern Europe and Yakutia. There might be a simple (and recent) expalanation for why Northeastern Europe is mostly "green" and Yakutia "red", but it would be nice to have actual datapoints in the quadrilater between NE Europe ("green"), SW Asia (mostly "red"), S Asia (zebu "black") and Yakutia.

PLoS ONE 6(1): e15922. doi:10.1371/journal.pone.0015922

Dual Origins of Dairy Cattle Farming – Evidence from a Comprehensive Survey of European Y-Chromosomal Variation

Ceiridwen J. Edwards et al.

Abstract
Background
Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages.

Methodology and Principal Findings
Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula.

Conclusions
We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.

Link

French cattle in global genomic context

The congruence of cattle breeds with inferred clusters is remarkable. K=47 frappe analysis is probably testing the limits of human visual perception...

PLoS ONE 5(9): e13038. doi:10.1371/journal.pone.0013038

Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

Mathieu Gautier et al.

Abstract
Background
Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time.

Methodology/Principal Findings
This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework.

Conclusions/Significance
Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations—the African taurine, the European taurine and zebus—may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence.

Link

Genomics reveal demographic history of cattle populations

The genomic distinction between B. taurus and B. indicus populations was also detected in another recent paper.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2531-9.

Cattle demographic history modelled from autosomal sequence variation.

Murray C, Huerta-Sanchez E, Casey F, Bradley DG.

Abstract

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus, with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus. Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

Link

Genetic structure of cattle in Eurasia

The mixed (east-west) affiliation of Mongolian cattle parallels the mixed affiliation of Mongolians themselves. The Caucasoids do not appear to have penetrated east of Lake Baikal, and some Caucasoid-influenced populations that live to the east of that frontier are thought to have originated there. Thus, the evidence from cattle complements that from physical anthropology and human population genetics to fix the border between the Western and Eastern Eurasian spheres of influence.

Anim Sci J. 2010 Jun 1;81(3):281-9.

Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers.

Lin BZ, Sasazaki S, Mannen H.

Abstract

The purpose of this study was to assess genetic diversity, phylogenetic relationship and population structure among nine Eurasian cattle populations using 58 single nucleotide polymorphism (SNP) markers. The calculated distribution of minor allele frequencies and heterozygosities suggested that the genetic diversity of Bos indicus populations was lower than that of Bos taurus populations. Phylogenetic analyses revealed the main divergence between the Bos taurus and Bos indicus populations, and subsequently between Asian and European populations. By principal components analysis, the Bos taurus and Bos indicus populations were clearly distinguished with PC1 (61.1%); however, six Bos taurus populations clustered loosely and the partial separation between European and Asian groups was observed by PC2 (12.5%). The structure analysis was performed using the STRUCTURE program. Distinct separation between Bos taurus and Bos indicus was shown at K = 2, and that between European and Asian populations at K = 3. At K = 4, 5 and 6, Mongolian population showed an admixture pattern with different ancestry of Asian and European cattle. At K = 7, all Bos taurus populations showed each cluster with little proportion of admixture. In conclusion, 58 SNP markers in this study could sufficiently estimate the genetic diversity, relationship and structure for nine Eurasian cattle populations, especially by analyses of principal components and STRUCTURE.

Link

Lactase persistence spread with Neolithic Linearbandkeramik

From the paper:

Following acceptance at the 0.5% level and regression adjustment we found that the most probable location where an LP allele first underwent selection among dairying farmers lies in a region between the central Balkans and central Europe (see Figure 3). It should be noted that, as simulated, we did not attempt to identify the location where the LP −13,910*T allele first arose. Instead we assumed that it started to rise to appreciable frequencies only after selection began among dairying farmers, initially at the particular location we estimated. The timing of the start of this gene-culture coevolution process was therefore strongly influenced by the arrival time of dairying farmers at the location where selection began in simulations. Since we selected simulations that give a good fit to the timing of the arrival of farming at different locations [31], we estimated a narrow range of dates for when selection began (95% CI 6,256 to 8,683 years BP;

...

Although not strictly a parameter of the model presented we have applied the ABC approach to estimate the genetic contribution of people living in the deme where LP-dairying gene-culture coevolution began, and its 8 surrounding demes, to the modern European gene-pool (95% CI 2.83 to 27.4%; mode = 7.47%; see Figure 4B) ... We then compared the distributions of genetic contribution (of people living in and around the LP-dairying start deme to the modern European genepool) with and without selection acting. To our surprise the two distributions are nearly identical.

In other words, selection for the lactase persistence allele did not result in modern Europeans having a larger proportion of their ancestry from the place where this process began.

From the paper:

Perhaps the most interesting result presented here is our estimation of the geographic and temporal origins of LP-dairying co-evolution. We find the highest posterior probabilities for a region between the central Balkans and central Europe (see Figure 3). At first sight such a location of origin may seem counter intuitive since it is far-removed from Northwest Europe, where the −13,910*T allele is found at highest frequency. However, previous simulations have shown that the geographic centroid of allele can be offset from its location of origin, particularly when it occurs on the wave front of a demographic expansion [29],[30]. The lactase-dairying coevolution origin region inferred here is consistent with a number of archaeologically attested patterns concerning the emergence and spread of dairying. Recent carbon isotope ratios from lipids extracted from archaeological sherds show the presence of milk fats in present-day western Turkey and connect these findings to an increased importance of cattle herding [26], [45]–[48]. In general, the spread of the Neolithic lifestyle from the Aegean to Central Europe goes hand in hand with the decline of the importance of sheep and goat and the rise in frequency of cattle bones in archaeological assemblages. While the Balkans at the beginning of the Neolithic still shows a variety of subsistence strategies [49], the middle Neolithic in SE-Europe and the earliest Neolithic in Central Europe after 7,500 BP show a clear preponderance of cattle.

A related recent study: Demography and selection in the spread of Lactase persistence in Europe (Gerbault et al. 2009)

UPDATE (Aug 29):

John Hawks raises two objections to the current paper:

There's only one little problem: It's hard to see how the same scenario gets the allele to India. Or, for that matter, Ireland. The authors posit that Indian lactase persistence will be found to be caused by a "diversity" of alleles. They seem to have missed this paper that found a greater diversity of lactase-associated haplotypes "north of the Caucasus" -- consistent with an initial steppe dispersal. OK, that's two problems, and they're not little.

I don't really see a problem with the spread of the allele to Ireland or to India. What the authors of this paper claim is that the allele began to be selected in Central Europe, not that it originated there. Its presence in Ireland or India does not strictly require any population movements from Central Europe. But there is also a plausible case for gene flow from Central Europe to either direction (Celts in the case of Ireland, and small-scale European admixture routinely detected in admixture studies that include South Asian populations).

As for the cited paper, it completely lacks samples from Central Europe, the Balkans, and Anatolia, hence its conclusion that the allele originated "north of the Caucasus" is spurious, and is not incompatible with the current paper which proposes a Balkan/Central European beginning of its selection process.

UPDATE (Aug 31)

John Hawks suggests in the comments that inclusion of South Asia into the model would shift the place of origin of the allele towards the east, and away from Central Europe. I do agree that a full model should account for the presence of allele as far as India or Central Asia. However, I doubt that their inclusion would have a major effect, for two reasons:

• Higher allele frequency in northwestern Europe compared to India suggests that the "point of origin" ought to be closer to the former than to the latter, or that the allele's selection began earlier in the former than in the latter.
• We must account for terrain and mode of transmission. The steppelands stretching from eastern Europe to the outskirts of China, combined with the invention of full pastoral nomadism made it possible for the spread of genes at a speed impossible for regular "demic diffusion". Moreover, a great part of this territory was essentially devoid of previous populations, and, the economy of the nomads necessitated its continued positive selection. Thus, the allele's frequency would not have been diluted by the time it reached the eastern ends of its expansion.

Thus, once the allele spreads to eastern Europe, the rest of the trip is -by comparison- a free ride.

The opposite trip (introduction to Europe from eastern European nomads) is also possible, but there are reasons to doubt this:

• The beginning of selection inferred in the current study is much older than the invention of pastoral nomadism. Inclusion of more populations could only push the time further into the past; it could not make it more recent. Thus, advocates of an "eastern" solution must explain how an allele appears to have started experiencing selection in the geographical region examined in the current paper thousands of years before it was introduced from the east.
• An eastern-western mode of transmission would result in an eastern-western cline, not a northern-southern one. An additional mechanism would need to be invoked to explain the latter.

PLoS Comput Biol 5(8): e1000491. doi:10.1371/journal.pcbi.1000491

The Origins of Lactase Persistence in Europe

Yuval Itan et al.

Abstract

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on −13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.

Link

Artificial selection in dairy cattle

PLoS ONE 4(8): e6595. doi:10.1371/journal.pone.0006595

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

Laurence Flori et al.

Abstract

Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways and regions which were affected by this selection. After analyzing the population structure, we estimated FST within and across the three breeds for each SNP under a pure drift model. We further considered two different strategies to evaluate the effect of selection at the genome level. First, smoothing FST values over each chromosome with a local variable bandwidth kernel estimator allowed identifying 13 highly significant regions subjected to strong and/or recent positive selection. Some of them contained genes within which causal variants with strong effect on milk production traits (GHR) or coloration (MC1R) have already been reported. To go further in the interpretation of the observed signatures of selection we subsequently concentrated on the annotation of differentiated genes defined according to the FST value of SNPs localized close or within them. To that end we performed a comprehensive network analysis which suggested a central role of somatotropic and gonadotropic axes in the response to selection. Altogether, these observations shed light on the antagonism, at the genome level, between milk production and reproduction traits in highly producing dairy cows.

Link

Genetic diversity of European cattle breeds

Mol Ecol. 2009 Jul 31. [Epub ahead of print]

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.

Medugorac I, Medugorac A, Russ I, Veit-Kensch CE, Taberlet P, Luntz B, Mix HM, Förster M.

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.

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mtDNA and Y chromosomes of Eurasian cattle

Heredity doi:10.1038/hdy.2009.68.

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus).

Kantanen J et al.

Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.

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Multifaceted origin of cattle revealed by DNA (Achilli et al. 2009)

PLoS ONE doi:10.1371/journal.pone.0005753

The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome

Alessandro Achilli et al.

Abstract

A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

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Haplotype block structure in the cattle genome

Related:

• Inbreeding/selection and cattle domestication
• Genome of cattle breeds
• Y chromosomes of Neolithic cattle do not suggest hybridization with European aurochsen
• Paleogenetics of cattle domestication

BMC Genomics doi:10.1186/1471-2156-10-19

High-resolution haplotype block structure in the cattle genome

Rafael Villa-Angulo et al.

Abstract

Abstract (provisional)
Background

The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use.

Results

From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1-100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure.

Conclusions

This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1-100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.

Link

Inbreeding/selection and cattle domestication

Related:

• Genome of cattle breeds

BMC Genomics 2009, 10:181doi:10.1186/1471-2164-10-181

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle.

Sean MacEachern et al.

Abstract (provisional)

Background

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the completion of the cattle genome, private companies are now providing large numbers of polymorphic markers for probing variation in domestic cattle (Bos taurus). We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP) in beef (Angus) and dairy (Holstein) cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in domestic cattle.

Results

Outgroup species: Bison, Yak and Banteng, were genotyped with high levels of success (90%) and used to determine ancestral and derived allele states in domestic cattle. Frequency spectrums of the derived alleles in Angus and Holstein were examined using Fay and Wu's H test. Significant divergences from the predicted frequency spectrums expected under neutrality were identified. This appeared to be the result of combined influences of positive selection, inbreeding and ascertainment bias for moderately frequent SNP. Approximately 10% of all polymorphisms identified as segregating in B. taurus were also segregating in Bison, Yak or Banteng; highlighting a large number of polymorphisms that are ancient in origin.

Conclusions

These results suggest that a large effective population size (Ne) of approximately 50,000 or more existed in B. taurus since they shared a common ancestor with Bison, Yak and Banteng > 1 million years ago (MYA). More recently Ne decreased sharply probably associated with domestication. This may partially explain the paradox of high levels of polymorphism in Domestic cattle and the relatively small recent Ne in this species. The period of inbreeding caused Fay and Wu's H statistic to depart from its expectation under neutrality mimicking the effect of selection. However, there was also evidence for selection, because high frequency derived alleles tended to cluster near each other on the genome.

Link

Genome of cattle breeds

The part I put in bold is interesting, as humans are themselves a "self-domesticated" species.

From the paper:

Our high resolution examination of cattle shows that unlike the dog—which has restricted diversity and high levels of inbreeding—domesticated cattle had a large ancestral population size and that more aurochs must have been domesticated than wolves; reducing the severity of the domestication bottleneck. SNP diversity within taurine breeds was similar to that of humans, but was significantly less than diversity within indicine breeds, which suggested that the Indian subcontinent was a major site of cattle domestication and predomestication diversity. Selection first for domestication and then for agricultural specialization have apparently reduced breed effective population sizes to relatively small numbers.

Related:

• Y chromosomes of Neolithic cattle do not suggest hybridization with European aurochsen
• Paleogenetics of cattle domestication

Science doi:10.1126/science.1167936

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

The Bovine HapMap Consortium

Abstract

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.

Link

Y chromosomes of Neolithic cattle do not suggest hybridization with European aurochsen

A previous study (pdf) had proposed that there was Y-chromosome evidence for introgression of native European Y-chromosomes into Neolithic cattle. Some previous posts on the mtDNA evidence.

From the paper:

In conclusion, the ancient distribution of the Y1 and Y2 haplotypes suggests that they do not discriminate European and Near Eastern Y-chromosomal lineages. As a consequence, there is still no patrilinear marker for investigating possible male introgression between imported cattle and European aurochs. So far, the importation of taurine cattle from its Near Eastern centre of domestication into Europe without subsequent hybridisation with local wild cattle populations remains the preferred model for the origin of European cattle.

From this paper, Figure 1 has the "Assumed distribution of aurochs mt-haplogroups in Western Eurasia", Figure 2 has the ancient Y data.

PLoS ONE 3(10): e3418. doi:10.1371/journal.pone.0003418

Y-SNPs Do Not Indicate Hybridisation between European Aurochs and Domestic Cattle

Ruth Bollongino et al.

Abstract

Background

Previous genetic studies of modern and ancient mitochondrial DNA have confirmed the Near Eastern origin of early European domestic cattle. However, these studies were not able to test whether hybridisation with male aurochs occurred post-domestication. To address this issue, Götherström and colleagues (2005) investigated the frequencies of two Y-chromosomal haplotypes in extant bulls. They found a significant influence of wild aurochs males on domestic populations thus challenging the common view on early domestication and Neolithic stock-rearing. To test their hypothesis, we applied these Y-markers on Neolithic bone specimens from various European archaeological sites.

Methods and Findings

Here, we have analysed the ancient DNA of 59 Neolithic skeletal samples. After initial molecular sexing, two segregating Y-SNPs were identified in 13 bulls. Strikingly, our results do not support the hypothesis that these markers distinguish European aurochs from domesticated cattle.

Conclusions

The model of a rapid introduction of domestic cattle into Central Europe without significant crossbreeding with local wild cattle remains unchallenged.

Link

Non-local Neolithic cattle remains near Stonehenge

The non-local origin of the cattle emphasizes the importance of the site, as it could draw prosperous cattle-owning visitors from afar. Together with the recent story on the Stonehenge fence, and its status as an elite burial ground, it appears that this was an important nexus of religious activity.

Stone-age pilgrims 'held barbecues at Stonehenge'

Analysis of animal remains found near to Stonehenge has shown that cattle were brought to the area from as far away as Wales or even the Scottish Highlands.

Scientists tested the chemical fingerprint of cattle teeth found at Durrington Walls, a Neolithic monument built 500 years before Stonehenge.

They found that far from being local, the animals could only have been reared in areas of Wales or Scotland, which have high levels of the chemical element strontium in the soil.

...

Dr Jane Evans, from the British Geological Survey who carried out the research, said: "It looks like people were driving cattle to the area from a significant distance away.

"The area must have been an important place for rituals and gatherings long before the first stones were laid at Stonehenge itself.

"People are coming from considerable distances and dispersion in order to have feasts and were bringing their own food supplies for what must have been a kind of bring your own beef barbecue."