The Mitochondrial Eve
The concept of a 'mitochondrial eve' is a concept that has been around in human terms for some time.
The idea is that we as humans all trace faithfully back to one female, or the 7 Daughters of Eve if you have read Bryan Sykes interesting novel on human mitochondria, and it is borne about by one of the principal achievements of mitochondrial genetics, which is the classification of all modern Europeans into seven groups, the mitochondrial haplogroups. Each haplogroup is defined by a set of characteristic mutations on the mitochondrial genome, and can be traced along a person's maternal line (your mother, to her mother, to her mother, etc) right back to a specific prehistoric woman. In his book, Sykes refers to these women as "clan mothers" (subsequent research has identified 29 of these and this is just in Europe) and all these women in turn shared a common maternal ancestor, the Mitochondrial Eve.
In terms of horses we have had similar attempts at classifying the mitochondrial lineage, although it must be said that the early protagonists, the likes of Goos, Franzel, Lowe and Bobinski, who faithfully arranged the thoroughbred in terms of female families using numbers, had no idea that their arrangement had genetic merit and certainly didn't do their work on that basis. The complete mitochondrial DNA sequence of the horse was first discussed by Xu & Arnason (Gene; 1994), and there has subsequently been a lot of papers discussing the phylogeny of the horse including some interesting papers including Jansen (Proc. Natl Acad. Sci 2002) and Ceislak (PlosOne; 2010). In regards to the thoroughbred, in terms of history Bower (Biol. Letters 2010) has written some interesting papers but commercially, in some sense, the most relevant papers for the thoroughbred industry have been that of Hill (Int. Soc for Animal Genetics; 2002), which first discussed errors in the stud book in terms of the Lowe/Bobinski/Shirai numbering, and then Harrison (Mitochondrion, 2006) who looked outside the d-loop and towards athletic potential (mitochondria after all is important in cellular respiration). There is a paper by Binns, et al entitled "Thoroughbred mitochondrial DNA reveals closer than expected links between maternal genetic history and pedigree records" that has been submitted to the Equine Veterinary Journal that looks particularly interesting in this vein.
It seems now, that following the work of Jansen and Ceislak, a research team headed by Alessandro Achilli, a researcher in the department of cellular and environmental biology at the Universita di Perugia in Italy, has analyzed equine mitochondrial DNA to find its own Mitochondrial Eve. The paper, which was released today and is free to download, outlines an interesting history of wild horses (equus ferus) living throughout Europe and Asia during the Paleolithic period. The authors note that many of the different mitochondrial haplotypes, and thus differing breeds, probably didn’t survive the peak of the last glacial period, from 26,500 to 20,000 years ago and another later period that covered Europe in ice. The study revealed 18 major haplogroups (A–R) across all breeds (so strictly speaking the concept that there are 50+ female families in terms of Shirai numbers in the thoroughbred is not correct), and the root of the tribe corresponding to an Ancestral Mare Mitogenome born approximately 130–160 thousand years ago. All haplogroups were detected in modern horses (E. caballus) from Asia, but the F haplogoup was only found in E. przewalskii—the only remaining wild horse.