Category Archives: bovine genetics

Qualifying diversity in bovine cattle

There is a new open access paper for all those with interest in the genetic history of cows:
Deirdre C. Purfield et al., Runs of homozygosity and population history in cattle. BMC Genetics, 2012. Open access ··> LINK [doi:10.1186/1471-2156-13-70]
The runs of homozygosity (ROH) are used to qualify the nature of the inbreeding (endogamy) process where it exists. When the ROHs are short (for example among Malagassy Zebu), that indicates that the genome has been recombined and fragmented many times, while when the ROH are longer, it can be inferred that inbreeding process is recent, as happened in Jersey and Guernsey, who applied strict cattle regulations since the 19th century.

Fig. 6 – minimally annotated by me

Figure 6 Average sum of Runs of Homozygosity (ROH) per bovine SNP50 animal <20 Mb in length within breed VS average sum of ROH >20 Mb in length. Breeds that originate from the same geographical area tend to cluster together with African Bos taurus breeds showing low levels for both measures, except for the Somba, Oulmès Zaer and Lagune breeds where elevated levels were clearly highly influenced by long ROH whereas the zebu breeds showed intermediate values of ROH but these were more strongly influenced by shorter ROH

The full names of the breeds are:

  • African taurines: Baoule (BAO), Lagoude (LAG), N’Dama (NDA), Oulmès Zaer (OUL),  Somba (SOM)
  • African hybrids: Kuri (KUR), Sheko (SHK)
  • African zebu: Zebu Bororo (ZBO, Zebu Fulani (ZFU), Zebu from Madagascar (ZMA)
  • British Isles: Angus (ANG), Guernsey (GNS), Hereford (HFD), Jersey (JER), Red Angus (RGU)
  • Northern Europe: Bretonne Pied Noire (BPN), Holstein-Friesian (HOL), Maine-Anjou (MAN) Maraichine from Parthenaise (MAR), Monbeliard (MON), Normande (NOR), Norwegian Red Cattle (NRC), French Pied Rouge Lowland (PRP)
  • Central/SW France: Aubrac (AUB), Charolais (CHL), Charolais from UK (CHA), Gascon (GAS), Limousin (LMS), Salers (SAL)
  • Alpine: Abondance (ABO), French Brown Swiss (BRU), Brown Swiss (BSW), Piedmontese (PMT), Romagnola (RMG), Tarine (TAR), Vosgienne (VOS)
  • Zebus: Beef Master (BMA), Brahman (BRM), Gir (GIR), Nelore (NEL), Santa Gertrudis (SGT)

Leave a comment

Posted by on August 17, 2012 in autosomal DNA, bovine genetics


Cow lineages in Europe, Africa and creole America

Another paper on bovine mtDNA adds important information to better understand the major matrilineage of domestic bovine cattle: haplogroup T1.

Importantly, Bonfiglio made a significant effort in sampling Egyptian and Ethiopian cattle, as well as some Latin American breeds. Not a single haplogroup outside of T1 was found, unlike in Europe where P, Q and R lineages do exist, suggesting some level of hybridization with wild aurochsen. There is however some uncertainty as for the exact phylogeny of haplogroups T1e (European) and T1f (Euro-Egyptian), which could also be branches of T1’2’3, as illustrated in fig. 1:

click to expand
The authors conclude that, soon after domestication in West Asia, bovine cattle spread to both Europe and Africa, where experienced secondary expansions, as evidenced by at least one lineage (T1d) looking East African by origin. 
That is also probably the case of T1c (Euro-Egyptian but more diverse in Egypt) and T1b (also most basally diverse in Egypt), which is the origin of the African-derived American “AA” haplotype of Paraguayan cattle, which is within this lineage.

Dated to 15,000 BP or older (source)

Update(Jun 10): There is abundant evidence in form of rock art and some remains at Jebel Uweinat, Qurta and Wadi Qubaniya supporting presence of wild taurine cattle in NE Africa since at least 15,000 BP. This allows for a possible semi-independent domestication event in Africa for bovids (h/t to Marnie).


Echoes from the Past (Mar 16)

You know: the stuff that should have been commented if I was perfect or a paid professional – but was not:

Pigmentation reasonably predicted
Yan Klimentidis mentions today that, according to a new paper (Cerqueira 2012, pay per view) as much as 64% of skin pigmentation can be predicted from genes (many of them), reaching to as much as 94% with freckles. The rate of success is much lower however for hair and eye color (44% and 36% respectively).
Are Ethiopians genetically adapted to high altitudes?
I’m generally skeptic of claims of genetic adaption to high altitudes when it does not seem to have ever been demonstrated that this adaption is genetic and not just mere biological flexibility caused by living in the area since childhood. In any case, L. Scheinfeldt 2012 (open access) claims that some candidate genes have been identified for the Amhara.
Taurine cattle could descend from as few as 80 female founders ··> R. Bollognino 2012 (ppv).

Human Evolution
Honey and human evolution: surely you never thought about it before, right? Nutritional anthropologist A. Crittenden thinks that honey may have been more important than meat, based on Hadza practices, which include symbiosis (cooperation) with a bird ··> The Rebel Yell.
Did prehistoric climate change affect human evolution the same as other animals? That is what J.R. Stewart and C.B. Stringer argue in a paper (ppv) ··> Science Daily.


Speculating about Still Bay culture (South Africa) and climate change ··> article by archaeologist J. Tolleson at Nature.
These marks are the first evidence of humans in Ohio
First evidence of hunting in Ohio c. 13,500 years ago ··> Cleveland Museum of Natural History.
Universal rock art script? David Sánchez mentions again[es] (I commented in 2010 too) the unusual hypothesisi of G. von Petzinger on the possibility that some sort of universal script used by hunter-gatherers around the world, as the markings on the walls appear to be roughly the same everywhere. I am rather skeptic though but curious anyhow. Among the links provided some are in English: video, The Guardian, New Scientist, UVic Space and Cambridge University.

Neolithic and Chalcolithic
One of the dolmens found in Alcónetar
Göbekli Tepe attracted worshipers from 500 kilometers around: from Cappadocia and the border of Armenia ··> Live Science. 
Some Neolithic settlers may have arrived to Iberia from North Africa (specifically Oran area) ··> Archaeology News Network.
Chalcolithic settlement found in Galicia, between Carballo and Berdoias, not far from the mamoa (dolmen) of O Valouco, as a highway was being built ··> La Voz de Galicia[es].
Two dolmens found in Alcónetar (Extremadura, Spain) as the water of the reservoir of Alcántara, one of the largest in Europe, recede because of unprecedented drought ··> Hoy[es].

Aurochs mtDNA challenges bovine phylogeny

Long horned european wild ox

New research has genotyped the ancient mtDNA of a wild aurochs from Italy. Importantly, the research challenges current understanding of Bos taurus phylogeny, suggesting that clades T1, T3 and T4 are paraphiletic, or more precisely: that they cannot be resolved phylogenetically to full satisfaction because:

Bayesian phylogenetic analysis of the European cattle and aurochs mtDNA coding genomes revealed that a model allowing for polytomies is strongly supported over a strict bifurcating model (Bayes Factor >100). Therefore, the pattern of previously classified bovid clades and sub-clades is not supported, suggesting that recurrent mutations and short internal branches may limit meaningful evolutionary information.

The aurochs sequence falls within T3 but the authors warn against this classification because of the issues mentioned before.

Aurochs mtDNA in Italian cattle

Aurochs fighting wolves by H. Harder
The same as Neanderthals did not completely go extinct but live in us (albeit in very small apportion), another magnificent creature from old also survived extinction by means of hybridization.
Mitochondrial DNA haplogroups known to be from ancient aurochs, whose last known representative died in 1627, have been discovered in Italian cattle, amounting to as much as 1.5% of the sampled individuals.
The lineages belong to three haplogroups: P, Q and R. P and Q had already been sequenced in pre-Neolithic European bovines (aurochs) but so far no P had been detected among modern cattle (in this case only one individual). A novel haplogroup, R, was also sequenced in several animals and, because of its even more archaic phylogeny, it is also believed to be an aurochs and not a domestic lineage.

Fig. 2 full Q, P and R sequences, including one from a British aurochs (18)