Iceman's sheep belonged to mtDNA haplogroup B

This establishes that the main mtDNA haplogroup (B) of extant European sheep was already present in the ~5.3ky old sheep hair shafts of the Tyrolean Iceman's clothing. The fact that the precise sheep sequence (like that of its bearer's) has not been identified in modern sheep testifies to the importance that drift and/or selection has played in the recent evolution of the species.

PLoS ONE 7(3): e33792. doi:10.1371/journal.pone.0033792

Phylogenetic Position of a Copper Age Sheep (Ovis aries) Mitochondrial DNA

Abstract Top

Background

Sheep (Ovis aries) were domesticated in the Fertile Crescent region about 9,000-8,000 years ago. Currently, few mitochondrial (mt) DNA studies are available on archaeological sheep. In particular, no data on archaeological European sheep are available.

Methodology/Principal Findings

Here we describe the first portion of mtDNA sequence of a Copper Age European sheep. DNA was extracted from hair shafts which were part of the clothes of the so-called Tyrolean Iceman or Otzi (5,350 - 5,100 years before present). Mitochondrial DNA (a total of 2,429 base pairs, encompassing a portion of the control region, tRNAPhe, a portion of the 12S rRNA gene, and the whole cytochrome B gene) was sequenced using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products. We have compared the sequence with the corresponding sequence of 334 extant lineages.

Conclusions/Significance

A phylogenetic network based on a new cladistic notation for the mitochondrial diversity of domestic sheep shows that the Otzi's sheep falls within haplogroup B, thus demonstrating that sheep belonging to this haplogroup were already present in the Alps more than 5,000 years ago. On the other hand, the lineage of the Otzi's sheep is defined by two transitions (16147, and 16440) which, assembled together, define a motif that has not yet been identified in modern sheep populations.

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

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

Retroviruses and the Origin of domesticated sheep

This paper suggests an "early" dispersal of sheep from the Near East, relics of which exist in peripheral areas, and a secondary major dispersal, also from the Near East, which is responsible for most modern sheep breeds.

Remnants of the earlier sheep breeds tend to have lower-quality wool, and this suggests that the secondary dispersal of sheep was associated with the beginning of the exploitation of the sheep's fur, rather than only its meat, resulting in the popularity of the new breeds.

It will be extremely exciting to track this dispersal archaeologically. We ought to have a few diagnostic SNPs of the various breeds of all the major domesticated animals very soon, which would be relatively easy to amplify in archaeological bone samples.

From the paper:

Collectively, the data we obtained indicate that relicts of the first migrations are still present in the Mouflon of Sardinia, Corsica, and Cyprus and in breeds in peripheral north European areas.

...

The homogeneous retrotypes (R2 only, or both R2 and R4) that we observed in the sheep of modern-day Turkey, Iran, Saudi Arabia, Syria, Israel, and Egypt, combined with available archaeological evidence, suggest that selection of domestic sheep with the desired secondary characteristics common to the modern breeds occurred first in Southwest Asia and then spread successfully into Europe and Africa, and the rest of Asia. [...] The primitive breeds survived the second migrations of improved breeds from Southwest Asia by returning to a feral or semiferal state in islands without predators or by occupying inaccessible areas less prone to commercial exchanges and associated introgression.

...

Our study also provides genetic evidence supporting the anecdotal origin of some less common sheep breeds. For example, one of the 10 populations analyzed from the British Isles, the Jacob sheep, displayed a homogeneous R2 retrotype very different from that of the other British populations and more similar to that of the southwestern Asiatic and African breeds [...] Our study also firmly links the Soay sheep with the Mediterranean and Asiatic Mouflon.

Science doi:10.1126/science.1170587

Revealing the History of Sheep Domestication Using Retrovirus Integrations

Bernardo Chessa et al.

Abstract

The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their "retrotype" and morphological traits dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as well as breeds previously recognized as "primitive" on the basis of their morphology, such as the Orkney, Soay, and the Nordic short-tailed sheep now confined to the periphery of northwest Europe. A later migratory episode, involving sheep with improved production traits, shaped the great majority of present-day breeds. The ability to differentiate genetically primitive sheep from more modern breeds provides valuable insights into the history of sheep domestication.

Link

First farmers in the Mediterranean

From the NY Times:

The invention of agriculture was a pivotal event in human history, but archaeologists studying its origins may have made a simple error in dating the domestication of animals like sheep and goats. The signal of the process, they believed, was the first appearance in the archaeological record of smaller boned animals. But in fact this reflects just a switch to culling females, which are smaller than males, concludes Melinda Zeder, an archaeologist at the Smithsonian Institution.


Using a different criterion, that of when herds first show signs of human management, Dr. Zeder finds that goats and sheep were first domesticated about 11,000 years ago, much earlier than previously thought, with pigs and cattle following shortly afterwards. The map, from her article in the August 11 issue of the Proceedings of the National Academy of Sciences, shows the regions and dates where the four species were first domesticated. Other dates, color-coded as to species, show where domesticated animals first appear elsewhere in the Fertile Crescent.

Here is the home page of Melinda Zeder, including a page on Animal domestication in the Near East with several older online papers.

From the paper:

Until the early 1990s Cyprus
was thought to have been colonized ca.
8,500 B.P. by a derived offshoot of fully
established Neolithic mainland cultures
(48). The new sites, however, date 2,000
years earlier (10,500–9,000 B.P.) and
document the arrival of early pioneers
hypothesized to have originated somewhere
in the Northern Levant (Figs. 1
and 2) (47, 49). Traveling the 60 k to
Cyprus by boat, these colonists transported
the full complement of economically
important mainland fauna (50).
including all four major livestock species
(sheep, goat, cattle, and pig).

Recent archaeological evidence from
the Aegean, for example, no longer supports
a model of gradual in-place transition
of ancestral Mesolithic cultures into
Neolithic cultures (53–55). Instead,
there appears to have been a sharp
decline in Late Mesolithic population
levels, combined with the sudden appearance
of radically different Neolithic
settlements in previously unoccupied
locations. As on Cyprus, recent work in
the Aegean argues for the arrival of
maritime colonists who, at ca. 9,000 to
8,000 B.P., carried many components of
the full Neolithic package (plant and
animal domesticates, new lithic traditions,
and, perhaps a bit later, pottery)
(Fig. 2). Following a leapfrog pattern,
these seafaring pioneers established
farming communities that selectively
focused on favorable environments in
coastal Greece and on various Aegean
Islands.

They argue that Neolithic lifeways
were introduced into the Italian peninsula
ca. 8,000 B.P. by maritime colonists
who first established farming villages on
the Apulian ‘‘boot heel’’ region of
southeastern Italy (Fig. 2). These traditions
appear in northwest coastal Italy
~200–300 years later (ca. 7,800–7,600
B.P.). In southern France, a compelling
case can be made for a marked geographic,
ecological, and cultural break
between interior Mesolithic settlements
and coastal Neolithic colonies (58) Recent
excavation of a coastal settlement
in southern France, dating to 7,700–
7,600 B.P. and characterized as a beachhead
colony of seafaring migrant farmers
from mainland Italy, has yielded
pottery, domestic sheep, einkorn, and
emmer wheat (59).

Having discounted evidence for piecemeal
cultural diffusion of various elements
of Neolithic economy and their
selective adoption by indigenous Mesolithic
populations in the western Mediterranean,
Zilha˜o (61, 62) has gone on
to demonstrate that, as in other parts of
the Mediterranean Basin, the Late Mesolithic
of the Iberian Peninsula was a
period of population decline and relocation.
Also as elsewhere, Neolithic settlements
with apparently fully formed
agro-pastoral economic systems suddenly
appear in the Iberian Peninsula as
coastal enclaves occupying limestonebased
soils abandoned by earlier Mesolithic
peoples.

Thus it appears that none of the earlier
models for Neolithic emergence in
the Mediterranean accurately or adequately
frame the transition. Clearly
there was a movement of people westward
out of the Near East all of the way
to the Atlantic shores of the Iberian
Peninsula. But this demic expansion did
not follow the slow and steady, allencompassing
pace of expansion predicted
by the wave and advance model.
Instead the rate of dispersal varied, with
Neolithic colonists taking 2,000 years to
move from Cyprus to the Aegean, another
500 to reach Italy, and then only
500–600 years to travel the much
greater distance from Italy to the Atlantic
(52).

PNAS doi: 10.1073/pnas.0801317105

Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact

Melinda A. Zeder

Abstract

The past decade has witnessed a quantum leap in our understanding of the origins, diffusion, and impact of early agriculture in the Mediterranean Basin. In large measure these advances are attributable to new methods for documenting domestication in plants and animals. The initial steps toward plant and animal domestication in the Eastern Mediterranean can now be pushed back to the 12th millennium cal B.P. Evidence for herd management and crop cultivation appears at least 1,000 years earlier than the morphological changes traditionally used to document domestication. Different species seem to have been domesticated in different parts of the Fertile Crescent, with genetic analyses detecting multiple domestic lineages for each species. Recent evidence suggests that the expansion of domesticates and agricultural economies across the Mediterranean was accomplished by several waves of seafaring colonists who established coastal farming enclaves around the Mediterranean Basin. This process also involved the adoption of domesticates and domestic technologies by indigenous populations and the local domestication of some endemic species. Human environmental impacts are seen in the complete replacement of endemic island faunas by imported mainland fauna and in today's anthropogenic, but threatened, Mediterranean landscapes where sustainable agricultural practices have helped maintain high biodiversity since the Neolithic.

Link

Cattle, sheep, and goats as endangered species

Why is genetic diversity in animals worthy of preservation? After all, if one has selected a super-breed of sheep that e.g., produces the best wool/expenditure ratio, why would one raise animals with suboptimal ratios? On the face of it, that doesn't make economic sense.

There is nothing wrong with doing that - in the short term. But, over time, you can expect that animals will be exposed to novel environmental challenges, e.g., changing climate, or food types, or newly evolved pathogens. Natural populations face these challenges by exploiting their existing genetic variation, changing in subtle ways to adapt to changing environmental conditions. By reducing genetic variation in a population, one is effectively reducing its ability to adapt to its environment.

Mol Ecol. 2008 Jan;17(1):275-84. Epub 2007 Oct 8.

Are cattle, sheep, and goats endangered species?

Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P.

For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources.

Link