Category Archives: horse genetics

Echoes from the past (August-28-2013)

Oh, yeah, I admit it: I have been procrastinating a lot. Result: an extremely long “to do” list. Naturally, I can’t make up for all the past laziness, so here goes a synthesis of what would otherwise be left unattended, take your time, please. 
Middle Paleolithic:
Atapuerca holds “uninterrupted” sequence of European humans since 1.2 million years ago. Soon-to-be-published theory of continuity from H. erectus to Neanderthals in the Castilian site → Paleorama[es], EFE Futuro[es].
More Neanderthal evidence for symbolism found in Fumane cave (Veneto, Italy): polished and ochre-painted shells (pictured) → PLoS ONE (open access), El neandertal tonto ¡qué timo![es].
Upper Paleolithic:
Epigravettian burial, dated to ~14,000 BP, found in Cuges-les-Pins (Provence). The Epigravettian (and not the more widespread Magdalenian) culture of this site indicates a direct link to Italy → INRAP[fr], La Provence[fr], Los Andes[es].
Oldest modern human remain of Galicia found at Valdavara cave (Becerreá, Lugo province). The milk tooth is 17,000 years old, 7000 years older than any other such finding in the NW Iberian country → Pileta[es], IPHES[cat].
Thousands of engravings, dated to c. 6000 years ago, found in Coahuila (Mexico) → RTVE[es].
“World’s oldest calendar” found in Scotland → BBC.
Female burial found at Poças de São Bento (Sado basin, Portugal) → Paleorama[es].
First farmers were inbred (at least in Southern Jordan) → Science Magazine.
Qatar Neolithic dig shows the peninsula was in contact with early Sumerian civilization (Eridu or Ubaid period, the first empire ever) → The Archaeology News Network.
Manure was already used by Europe’s first farmers → Science.
Haryana (India) town is oldest large IVC settlement → Business Standard.
East China engravings show first Oriental writing (~5000 years’ old, just slightly younger aged as Sumerian cuneiform writing but much more recent than the controversial Tărtăria tablets of Bulgaria) → The Guardian, English People.
North American natives caused lead pollution in Lake Michigan (oldest recorded) → PPV paper (ER&T)University of Pittsburg.
Perdigões enclosure and collective burial was pilgrimage center. Antonio Valera (often so scholarly cryptic at his blog) loosens up when interviewed by a Portuguese publication, giving meaning to the archeology he’s working with → Super Interesante[por].
Bronze Age:
Cypriot harbor city dug: Hala Sultan Tekke, near modern Larnaka, had 25-50 Ha. and was active between the 16th and 12th centuries BCE → The Archaeology News Network.

Also from Cyprus: large settlement dug out near Nicosia (Cyprus), dated to 2000-1500 BCE → The Archaeology News Network.
Human evolution:
Modern human shoulder much more efficient than chimpanzees’ at throwing… but also than H. erectus’ → BBC.
Neanderthals did speak (of course) → Science Daily, open access paper (Frontiers in Psychology).

Note: their unfounded insistence on most unlikely H. heidelbergensis shared origins of Neanderthals and us casts some doubt on elements of their reasoning however.

Record ancient DNA: ~700,000 years’ old horse sequenced → Nature Communications (PPV).
Experimental archaeology:
How to carve your own stone tools and weapons out of modern materials: very interesting videos (in English) at Paleorama[es] (scroll down). 
More tomorrow (nope my “to do” list is not at all finished with this entry).

Horse genetics (autosomal DNA)

Barb horses
(CC by Notwist)
Yet another paper on horse genetics is available these days.
Jessica L. Petersen et al., Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data. PLoS ONE 2013. Open accessLINK [doi:10.1371/journal.pone.0054997]


Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Regardless of what the authors claim, previous studies have suggested dual origins (steppes and local domestication at or near Iberia) or even multiple ones for modern horses and this paper’s data does not say otherwise but actually reinforces this notion. For example let’s have a look at their fig. 1 (duly annotated by me):

Ignoring by the moment the Latin American breeds, which stem directly from the root of the tree, the oldest division is between the Iberian breeds (Lusitano, Andalusian) and all others, which in turn split in two groups, both scattered in Europe and Asia (different parts of Asia however). This would seem to confirm the dual origins theory. 
However there are two more elements to consider: on one side the Northern Iberian breeds (apparently even older than the Southern ones, per Warmuth 2011) are not being considered here. 
The other element to ponder is the most strange position of the three Latin American breeds. As there were no horses in America at the arrival of Europeans, the origins of such anomaly must be in the Old World, meaning probably that these breeds retain genetics of even older populations. These could be the already mentioned Northern Iberian breeds but they are said to have some admixture from Berber horses (or Barb) as well and this population (argued to be very old) has not been subject to any genetic study as of now.

Hopefully future studies on the matter will consider these issues.

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Posted by on January 31, 2013 in horse genetics


Echoes from the Past (Jan 18)

Again lots of short news and hopefully interesting links I have been collecting in the last weeks:
Lower and Middle Paleolithic 
Cova del Gegant Neanderthal jaw
Catalonia: Neanderthal mitochondrial DNA sequenced for the first time. The sequence, obtained from a jaw from Cova del Gegant (Giant’s Cave), is fully within normal Neanderthal range ··> Pileta de Prehistoria[es], NeanderFollia[cat], relevant paper[cat] (PDF)

Castile: Stature estimates for Sima de los Huesos (Atapuerca) discussed by John Hawks.

Upper Paleolithic and Epipaleolithic

Romania: stratigraphies and dates revised by new study (PPV) ··> Quaternary International.

Andalusia: oldest ornament made of barnacle’s shell (right) found in Nerja Cave ··> Pileta de Prehistoria[es], UNED[es], Universia[es].

England: Star Carr dig to shed light on transition from Paleolithic to Epipaleolithic ··> short article and video-documentary (32 mins) at Past Horizons.

Basque Country: archaeologists consider a barbarity that only 65m are protected against the quarry at Praileaitz Cave (Magdalenian) ··> Noticias de Gipuzkoa[es].

Yemen: 200 tombs said to be Paleolithic discovered in Al Mahwit district, west of Sanaa. Tools and weapons were also found. Other thousand or so artifacts from the same period were found in the Bani Saad area  ··> BBC

Peruvian rock art
Sarawak: Niah Cave being dug again for further and more precise data on the colonization of the region by Homo sapiens ··> Heritage Daily.

Siberia was a wildlife-rich area in the Ice Age ··> New Scientist.

Peru: 10,000 years old cave paintings (right) discovered in Churcampa province ··> Andina.

Neolithic and Chalcolithic

Iberia and North Africa: Southern Iberian and Mediterranean North African early Neolithic could be the same process according to new paper (PPV) ··> Quaternary International.
Galicia: Neolithic and Metal Ages remains to be studied for DNA ··> Pileta de Prehistoria[es].
Texas: very informative burnt hut reveals clues of the natives of the San Antonio area c. 3500 years ago.
Mexico: 2000-years old paintings found Guanajuato ··> Hispanically Speaking News (notice that the photo appears to be act of shameless journalistic low quality, being a European bison painted with European style, probably from Altamira).
Metal ages and historical period
Croatia: oldest known astrological board unearthed at Nakovana (Roman period). The cave was probably some sort of shrine back in the day, maybe because a striking phallic stalagmite. Besides the ivory astrological device, lots of pottery has been found as well ··> Live Science.

The best preserved fragment depicts the sign of Cancer (full gallery)
Basque Country: Iruña-Veleia affair:  Basque autonomous police does not have means to test the authenticity of the findings. The Commission for the Clarification of Iruña-Veleia asks for the tests to be performed in one of the few European laboratories able to do that ··> Noticias de Álava.
Cornwall: replicating sewn-plank boats of the Bronze Age ··> This is Cornwall.
India: cremation urn from the Megalithic period excavated in Kerala ··> The Hindu.

Human genetics and evolution

The six flavors
Centenarians don’t have any special genes ··> The Atlantic.
Fat is a flavor: newly discovered sixth flavor in human tongue identifies fat (and usually likes it) ··> Science Daily.
Hominin tooth found in Bulgaria dates from 7 million years ago ··>  Daily Mail.
Anthropology (senso stricto)
The journey of the Tubu women: fascinating documentary in Spanish language about these trans-Saharan trader women available at Pasado y Futuro[es].
Small capuchin monkey bands fight as well as large ones because members are more motivated and have many less defections, even in peripheral conflicts  ··> Science Daily.
Horse genetics again ··> new paper at PLoS Genetics

Fig. 4 – Phylogenetic tree of extant Hippomorpha.

Horse domestication incorporated most wild horses, mtDNA suggest

Welsh Pony
A new paper on equine mitochondrial DNA, focusing on shedding light on the origins of domestic horse (Equus caballus) is available:

From the Results section:

Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.

As always, I have a general attitude of caution on molecular clock estimates (and in this case the authors agree with such precautionary attitude). So I take these figures as mere loose references, however the overall notion of most mitochondrial DNA being ample spectrum pre-domestic seems correct and has been demonstrated in the past.
This wide maternal ancestry seems to persist even within breeds. Only the Welsh pony of all breeds sample showed some tendency towards a single matrilineage. 

Bayesian Skyline Plot of effective population size through time based on the
whole mtDNA sequence from 63 horses. The beginning of the recent effective population
size expansion is marked in red (median 7,000 years BP).
Actually, if we take this estimated chronology at face value and use oly the median values (blue line), the expansion would seem to go strong only towards 6000 years ago, 4000 BCE, roughly the age of horse domestication per the usual archaeological understanding.

See also: category: horse genetics.

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Posted by on November 15, 2011 in Epipaleolithic, horse genetics, Neolithic


Echoes from the past (Aug 29) – various interesting news

Follow here a series of links and comments on issues that are of some prehistoric or genetic interest (plus a well fed section of astronomy news this time), which I have got no time to deal with so far… or do not come with enough info to merit a separate entry… or are not of great interest to me.
Neanderthal trowel at Abric Romaní (Catalonia)

Print and reconstruction of the trowel
The almost hollow print of what once was a trowel (or similar) has been found at the important Paleolithic cave of Abric Romaní (Capellanes, Catalonia). The print came with some residues which indicate that the instrument was left at the fire when it was already off, so it did only burn superficially, later being deprived of oxygen by water and moss. 
The artifact’s length is of 32 cm, with a maximum width of 8 cm and may have been used to manage the fire. It is dated to 56,000 years ago.
··> El Mundo[es], Neanderfollia[cat].
More mammoth petroglyphs in North America
I recently mentioned a mammoth engraving from Florida, which should be from c. 13,000 BP. Another place where such engravings seem to exist is San Juan River, near Bluff (Utah).
That is what Ekkehart Malotki and Henry D. Wallace argue in a paper published at Stone Pages, which includes many images of petroglyphs, only a few of which look like mammoths, one of them very clearly so.

The mammoth (left, eroded) has a bison partially superimposed (right)

Opium ritual and medicinal use in Iberian Neolithic

Ritual use was some times associated to these idols
The opium poppy grows spontaneously in most of Europe, specially in the Mediterranean. I was knowledgeable that Western Danubian farmers had grown and used this narcotic in Germany and nearby areas but this is the first explicit reference I know of its use in the Mediterranean basin or the Iberian peninsula.
Sadly this material is in Spanish language and I don’t have room nor time here to deal with it properly. Hopefully later on.
The evidence of use of this drug is analyzed in several sites, most of them in Andalusia but also from Catalonia…
Paleolithic findings from Triacastela, Galicia
Pileta de Prehistoria[es] also tells us of research in a relatively ill-documented region: Galicia. The findings at Triacastela are from the Middle Paleolithic (Neanderthals) and Upper Paleolithic (H. sapiens). From this last period a decorated dart has been found:

Documentary on destroyed archaeological site

The last bit I want to highlight from Pileta is a documentary (in Spanish) on the destruction by private businesspeople of the archaeological patrimony of the cave of Chaves (Aragon). I already mentioned this crime against humankind in 2010 at my old blog.
··> Chaves la Memoria expoliada (video at Pileta de Prehistoria, in Spanish, 55 mins).
Archaic immune introgression?
I mentioned in June some speculation on HLA (immune system) introgression from Neanderthals or other archaic Homo in Asia. The corresponding paper has been published with more data but is pay per view (supp. material is accessible however). Back in the day I thought it looked at least partly unlikely (as the corresponding haplotypes are in some cases found in Africa).
Przewalski horses at the origin of domesticated horse Y-DNA

While horse mtDNA is most diverse and suggests many origins, all known Y-DNA comes from a single lineage… which happens to be related to that of the Przewalski wild horses of Mongolia via an ancient intermediate lineage located at Tuva Republic.
Ancient wild horses from Siberia and Alaska however had much greater Y-DNA diversity.
··> Science Daily, Nature (PPV).
Tunisian lineages
Dienekes mentions two new papers on Tunisian Y-DNA (and one of them also on mtDNA), yet they are both pay per view and the announced results seem not really novel. Anyhow, for the reference, they are:
Snow White and the red apple

Artistic rendering of Snow White
Unnamed Dwarf Planet (Snow White 2007 OR10) gives us some new information on itself and the Kuiper Belt. To begin with Snow White happens to be red in fact, what requires some explanation. 
Mike Brown, the man who demoted Pluto and discovered Eris, Sedna and a host of other Transneptunian objects, explains it in detail in three successive entries at his blog: The redemption of Snow White (part 1, part 2 and part 3).
Also news story at Science Daily.

Panspermia? Yes but from Earth outwards

Panspermia is the theory that proposes that life (in its primitive forms) may have arrived to Earth from outer space. Modeling of meteorite impacts however suggest that the opposite may also be true. These impacts could well have ejected materials with terrestrial life such as bacteria or even those hardy water bugs known as tardigrades, which can withstand almost anything.
So ‘earthling’ life may already exist on Mars, Venus or other planets, moons or asteroids of the Solar System… and there was no need for human-made spacecrafts for them to make such journeys. 
Direct evidence will have to wait however: it is just a model.
··> BBC.
    Diamond planet
    Extremely compressed carbon seems to be what a planet, once a white dwarf star, is made of. That is like saying that the whole planet is the largest known diamond ever. 
    Sadly for those thinking about mining it, it lays at 4000 light-years of distance, 1/8 of the path from here to the Galactic Center.
    ··> SD.


    Horse’s double origins

    Pootok arra Orbelaunen
    The archaeological evidence was very much inconclusive in this matter of where modern horses originated. While horses were obviously central to Paleolithic cultures of SW Europe, who ate and painted them with almost religious devotion, since the end of the Ice Age and until the Metal Ages there is a fossil gap on horses, not just in SW Europe but also everywhere else.
    Then the first domestic horses show up in the Eurasian steppes, north of the Caspian Sea, (notably Botai culture but also Samara and Dniepr-Don) and there is a clear expansion of this animal along the routes taken by the Indoeuropean invaders of the Kurgan cultural phenomenon.
    In this sense, some believed that horses had gone extinct in SW Europe upon the arrival of Holocene. A new paper challenges this idea based on genetic diversity:


    The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.
    BGD Ranch's Caspians
    Caspian horse
    Notice that all but one of the samples from the Iberian peninsula are from the North and that also Occitan horse breeds like the famous Camargue show very high diversity. Hence talking of Iberian refugium may be a misnomer and we should better talk of SW Europe.
    In the Eastern area, there is a limitation of sampling sites, with only two breeds representing all the potential diversity once extant in Eastern Europe, West and Central Asia. These are the Caspian horse from Northern Iran and the Ahal Teke breed from Turkmenistan (also very popular in Russia and the North Caucasus).
    The essence of the results of this study is visible in fig. 1:

    3 horses on pasture
    Following table 2, the highest genetic diversity (Nei’s H) of all surveyed breeds corresponds to the Occitan and Basque horse breeds: Camargue and Pottoka (H=0.776 and H=0.775 respectively). Follow closely the Caspian horse of Iran (H=0.770) and the Garrano of Portugal (H=0.763) and the Galician horse (caballo gallego, H=0.762).
    Another way to measure diversity is allelic richness (Rs). By this measure, the most outstanding breed is the Galician horse (6.82), followed by the Caspian horse (6.70), Garrano (6.56), Pottoka (6.52) and Camargue (6.43).
    Overall we find that these five breeds cope all the highest diversity positions, being all from SW Europe, except the Caspian horse.

    Caballo tipico gallego
    Galician horse

    See also in this blog: Horse had multiple domestication events (ancient equine mtDNA) (Dec 2010).


    Posted by on April 1, 2011 in European prehistory, horse genetics, Neolithic


    Horse had multiple domestication events (ancient equine mtDNA)

    German researchers have successfully retrieved mtDNA from 85 ancient specimens from diverse Eurasian regions and periods, ranging from c. 12,000 BCE to the Middle Ages. They have found that most of the extant mtDNA diversity in the species existed before domestication.

    Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.

    The paper provides ample insight on the various haplotypes and where they are found first. Not all lineages are from the putative area of first domestication (the Eurasian steppe) but they are also from other regions (East Asia, mainland Europe, Iberia).

    Fig. 2 – Ancient horse mtDNA haplotypes with timeline and region

    They also researched primitive horse breeds. 39 haplotypes were confined to one of these breeds. Among them are notable those of the Iberian peninsula (Lusitano, Marismeño, Cartujano, Garrano), which appear to have roots in pre-Neolithic local wild horses. Similarly the Basque pony known as pottoka also has roots in ancient mainland European horses (X1, derived from D). [Correction (Apr 6 2011): Pottoka’s matrilineage X1 is of apparent Siberian origins: C – only attested in one individual. X1 as such is only documented since the Iron Age, in mainland Europe].
    Other primitive breeds with unique haplotypes are Arabian, Cheju, Akhal Teke, Sicilian Oriental, Yakut, Debao and Fulani. The authors argue that the Altai Mountains and the Takla Maklan and Gobi deserts were barriers partly impeding the genetic flow from the Eurasian steppe to East Asia, where several of these breeds belong.

    Update (Apr 6 2011): see also to this more recent post: Horse’s double origins, on new research supporting by means of autosomal DNA diversity the double origin in the steppes and SW Europe of modern horses. 

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    Posted by on December 22, 2010 in aDNA, Eurasia, horse genetics, mtDNA