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Equine Genetic Genealogy
 


Six things you may not know about
mitochondria and equine mtDNA

1. According to the Endosymbiotic
Theory mitochondria orginated as a
cell-invading bacterium. Host and
parasite worked out a relationship
so mutually beneficial that now they
can't live without each other.

2. Equine sub-haplogroup L1 is
considered by some to be the
Ancestral Iberian Haplogroup.

3. L1 more likely represents a first
millenial restocking of the Iberian
peninsula. Another haplogroup
dominates in the oldest Iberian
horse remains.

4. Domestication may not have
agreed with the earlier Iberian clan.
Their haplogroup is extremely rare
in the contemporary horse population.

5. The oldest equine mtDNA
sequence comes from the 'Thistle
Creek [Yukon] horse' which had been
preserved in permafrost for
c700,000 years.

6. The HVS1 sequence of the
Thistle Creek horse and several
other sequences found in ancient
specimens are unknown in
the contemporary global horse
population, suggesting that the late
Pleistocene extinction of the wild
horse in the Americas and later
domestication in the old world
resulted in modest losses of
mitochondrial diversity.




Pedigree Matters

Deep-Rooted Anomalies in
Female Families




TB Mitochondrial DNA

Mitochondrial DNA is a snapshot of the distant matrilineal past. There horses (and other mammals) should resemble the dam of thirty, forty, or more removes about as closely as they do their mother. If comparison of mitochondrial 'photographs' of members of the same TB female family reveals one or more individuals that do not closely resemble the rest it is conclusive proof of error somewhere in the tail female pedigree record. If comparison of two or more different families reveals no difference in appearance it raises the possibility of, but does not prove, a common dam within the last thousand years or so.

Mitochondria are the power generators of the cell, present there in multiple copy, the actual number being commensurate with a cell's metabolic activity. The mitochondria have their own DNA in a single ring-shaped chromosome, enabling them to reproduce independently of the cell itself. The mitochondrial chromosome of the domestic horse contains 16,660 nucleotides, over 90% of which control protein synthesis (the "coding region"). The remainder is the displacement loop (d-loop) where the chromosome opens for transcription, also known as the "non-coding" or control region.

MtDNA is inherited exlusively from the mother. Any paternal mitochondria that are not expended prior to fertilization are normally inactivated at that time. Lacking a paternal analogue there is effectively no recombination. The only way mtDNA changes is via spontaneous mutations. Such mutations do regularly occur. The average overall rate of mutation in mtDNA is measured in thousands of years. If present in a germ cell mutations persist in subsequent generations. Mutations in the coding region often result in functional problems for the organism. These are less likely to persist than mutations in the d-loop. Within the d-loop are two sections which exhibit a faster than average rate of mutation. These are known as hypervariable sections HVS1 and HVS2.

Sets of mutations shared by a large number of individuals define maternally-linked populations known as clades or haplogroups, several of which are large enough to have major subdivisions within them called sub-haplogroups. Within these, additional mutations define minor subdivisions and, finally, individual haplotypes. By comparing shared and non-shared mutations between two or more individuals a rough estimate can be made as to how long ago their most recent common ancestor (MRCA) in tail female lived. This has made mtDNA a very useful tool for studying the evolution of various species. It has also become a popular tool for human genealogical research.

It is equally useful for equine genealogical applications such as testing the accuracy of the record of the Thoroughbred female families. To date, four reports correlating TB female families with mtDNA haplotypes have been published. However, sequencing for three of them (Hill et al. 2002, Bower et al. 2012a, and Bower et al. 2012b) was limited to d-loop fragments, usually just partial HVS1. Paralleling the evolution of human mtDNA analysis, d-loop alone was initially regarded by many as sufficient for adequate haplotype definition but turned out to be insufficient for that purpose. As first reported anecdotally by Harrison & Turrion-Gomez 2006, Achilli et al. 2012 proved beyond any doubt that it’s frequently impossible to adequately define equine mtDNA haplotypes without information from the coding region.

Since 2012 many full mt TB sequences have been published through GenBank. While, unfortunately, none of them are identified by family number they nonetheless prove that the short partial HVS1 sequences used for the three aforementioned reports effectively masked considerable variation in the TB. What was first reported as a single haplotype, "F", by Hill et al. 2002 (Table 1) and subsequently (by segregation at an HVS1 indel excluded from previous consideration) was reported as two haplotypes by Bower et al. 2012b (Table 1, "Lineages 2, 8, 16" and "Lineages 7, 17, 22"), is actually no fewer than 4 different haplotypes as defined from full mt TB sequences. Bower’s "Lineages 10, 14, 42" (Hill’s "D") probably conflates two, possibly three haplotypes. "Lineages 6, 20, 23" (Hill’s "N") may conflate two haplotypes. Outside their Tables, Bower et al. 2012b effectively conglomerated ("Discussion" p.234) families 1, A1, and A4, conflating no fewer than two different haplotypes. So far, there is no evidence of conflation in the "Lineages 9 and 12" (Hill’s"G") and “Lineages 4, 11, 13” (Hill’s “J”) conglomerates although in HVS1 alone the former is distinguished from several other haplotypes only at mutational ‘hotspots’ which are the last resort in determining haplotype assignment.

Sequencing for the fourth TB study (Rogers, 2014) included certain markers in the coding region. The findings reported have clarified the phylogenetic relationships between the families (1, 25, A4) with typical haplotypes in haplogroup N and enabled specific definition of the typical haplotype for family 16, thereby resolving some of the conflation in the "Lineages 2, 8, 16" conglomerate. Full resolution of conflation in that and other conglomerates awaits further study. That is why two or more haplotypes are associated with some families/family branches in the table below which sets forth distribution of 27 haplotypes, presently regarded as representative of matrilineally unrelated foundation era mares, among and within the 31 numbered TB families (27 British, 4 American) sampled and reported publicly to date.

See also: "Distribution of Thoroughbred Matriarchs In the Equine Mitochondrial Tree


Family

Blue italics indicate a family or family branch in which two or more haplotypes are known to occur.

Haplogroup Assignment

Nomenclature of Achilli et al. 2012 as expanded by Peng et al. 2015

Remarks

(MRCA = the most recent common ancestor in tail female as defined by uncorrected final stud book record. A haplotype can reasonably be considered accurately representative of a lineage only as far back as the MRCA of a set of individuals tested and found to have that haplotype. In a few cases a family is represented only by a single contemporary individual tested. That information is of interest but effectively verifies the haplotype only as far back in the tail female lineage as the earliest dam foaled after the advent of parentage verification by DNA.)

1-a, 1-b, 1-c, 1-d, 1-e, 1-f, 1-g, 1-h, 1-I, 1-j, 1-k, 1-L, 1-m, 1-n, 1-o, 1-p, 1-r, 1-s, 1-t, 1-u, 1-w, 1-x N2a The MRCA of all individuals tested, of all that tested N2a (Rogers, 2014), and of all extant branches of family 1 is Bonny Lass (1723 Bay Bolton). Atypical haplotypes reported in some individuals tested from branches 1-k, 1-n, 1-p, and 1-u represent errors that entered the record during or since the last quarter of the 19th century. The only evidence for error in 1-k is the haplotype identified in the remains of Bend Or (1877 Doncaster). He was recorded as produce of the 1-k branch mare, Rouge Rose (1865 Thormanby), but did not have the expected N2a haplotype for family 1 as found in contemporary descendants of two or more of her daughters. The errors in 1-n and 1-p occurred at some point after the branch mares Chelandry (1894 Goldfinch) and Hilarity (1871 King Tom), respectively. The error in 1-u is at or after Whinbloom 1901 by Galeazzo (ibid.). Note:the 1-a individuals tested do not include any tail female descendants of imported Bonny Lass.
1-k, 1-n, 1-p L3a1b or L4a  
1-u L3a1b  
2-a I2a2a The MRCA of all individuals tested is Lusty Thornton (1710c Croft’s Bay Barb). Her dam Chesnut Thornton (1705c Makeless) is the MRCA of all extant branches of family 2. The findings place different haplotypes under Lusty Thornton’s daughters Ringbone (1732 Croft’s Partner) branch mare of 2-a, and Brown Woodcock (1717 Darcy’s Woodcock) as 2d dam of Miss Makeless (1737 Young Greyhound), the MRCA of all family 2 samples testing L4a (or L3a1b). An atypical haplotype found in some 2-f individuals indicates an error at some point after the branch mare (1804 by Hyacinthus), The haplotype expected for Miss Makeless’ descendants was reported (Bower et al. 2012b) as part of a 3 family conglomerate ("Lineages 2, 8, 16") that conflates two different haplotypes. Anecdotal information from the research community suggests that the haplotype expected for Miss Makeless’ descendants is L4a. See remarks for families 8 & 16.
2-d, 2-e, 2-f, 2-l, 2-n, 2-o, 2-s L4a  
2-f L1a  
3-b, 3-d, 3-e, 3-g, 3-l, 3-m, 3-n, 3-o L2b1a The MRCA of all individuals, all testing L2b1a, and all extant branches of family 3, is a mare (1735c) by Bartlett’s Childers. The MRCA of the four 3-c individuals reported (Bower et al. 2012b) as A1a is unknown. This finding indicates an error in the record that at present can be localized no more precisely than at or after Snapdragon (1759 Snap).
3-c A1a
4-c, 4-d, 4-j, 4-k, 4-l, 4-r I2a1 The MRCA of all individuals tested and publicly reported to date is Sister to Guy (1722 Greyhound). The MRCA of all extant branches in family 4 is her 2d dam, a mare by Brimmer.
5 H The MRCA of all individuals tested and of all extant branches of family 5 is Ebony (1728 Flying Childers). The MRCA of the 5-d and 5-e (B1a) samples is Sister to Fag (1780 King Herod) who traces to Ebony's daughter Hag (1744 Crab). The MRCA of the 5-g and 5-h (D1a2) samples is Miss West (1777 Matchem) who traces to Ebony's daughter Young Ebony (1742 Crab). A third haplotype (H) was found in one or more samples, lineage unspecified, from the 'trunk' of family 5 which is extant under all of Ebony's daughters except Hag. These findings indicate that the final GSB record (vol.1, ed.5) for the early generations of family 5 conflates no fewer than three separate matrilineages.
See: Deep Rooted Anomalies in Female Families Revealed by mtDNA Testing.
5-d, 5-e B1a  
5-g, 5-h D1a2  
6-a L2b1b The MRCA of all individuals tested and of all extant branches of family 6 is Charming Jenny (1690c Spanker). The findings place different haplotypes under two mares attributed to her, Cream Cheeks (1695c Leedes Arabian) the branch mare of 6-a, and Betty Percival (1705c Leedes Arabian) as 4th dam of the 6-b branch mare Horatia (1758 Blank), the MRCA of all individuals tested so far except those from 6-a. This indicates that the final GSB record (vol.1, ed.5) for the early generations of family 6 conflates at least two separate matrilineages. A third haplotype, the only one reported so far in branch 6-e, represents a more recent error in the record of Horatia's descendants that, since the MRCA of the 6-e individuals tested is unknown, can be localized no more precisely than as early as La Favorite (1863 Monarque) dam of the 6-e branch mare Fenella (1869 Cambuscan), or as late as Selene (1919 Chaucer).  
See: Deep Rooted Anomalies in Female Families Revealed by mtDNA Testing.
6-b, 6-d, 6-f M1a or M2  
6-e L3a1b or L4a
7, 7-a. 7-f L3a1a or L3a1a1 The MRCA of all individuals tested is unknown. The MRCA of all extant branches of family 7 is Miss Slamerkin (1729 Young True Blue).
8-a, 8-c, 8-d, 8-h L3a1b The MRCA of all individuals tested and of all extant branches of family 8 is a Mare (1695c) by Byerley Turk and out of the family 8 taproot, a mare (1690) by Bustler. Partial HVS1 sequences from contemporary 8-c samples do not all agree at a mutational ‘hotspot’. This should not be regarded as evidence of error without information from full mt sequences. Reported (Bower et al. 2012b) as part of a 3 family conglomerate ("Lineages 2, 8, 16") that conflates two different haplotypes. Anecdotal information from the research community suggests that family 8 has the same haplotype, L3a1b, as expected for family 16.
9, 9-a, 9-e, 9-f G2a or G2a1 The MRCA of all individuals tested, all individuals with a G2a haplotype, and of all extant branches of family 9 is a mare (1695c) by Curwen's Spot. The MRCA of all individuals with an L1a haplotype is Sister to Sloven (1728 Bay Bolton). This points to conflation of no fewer than two different matrilineages in the record of the early generations of family 9 as last published in the GSB (vol.1, ed.5). A third haplotype found in some  9-b individuals tested indicates an error at some point after the 9-b branch mare.
See: Deep Rooted Anomalies in Female Families Revealed by mtDNA Testing.
9-b, 9-c L1a
9-b L2a2a, L2a2b, or L2b1
10 (branch unknown) L2a2a or L2a2b The MRCA of all individuals tested is unknown. The MRCA of all extant family 10 branches is a Mare (1765c) by Snap.  (Hill et al. 2002 reported (Table 1) a single individual from family 10 (lineage unknown, no branches were specified in that report), as their haplotype "B" and 7 individuals from family 14 as their haplotype "D". Bower et al. 2012(b) conglomerates families 10, 14 and 42 (previously unsampled) into "Lineages 10, 14, 42", the haplotype for which as shown in Bower's Table 1 is identical to and specifically equated with Hill's "D". Hill's haplotypes "B" and "D" differ only at np 15827. Given their similar treatment Table 1 of Hill’s "B" and "Q" (de novo variant of their "G"), it appears that Bower et al. may have regarded "B" as a de novo variant of "D". However, "B" is actually identical in HVS1 to two TB haplotypes that are in a separate subdivision of sub-haplogroup L2 from the TB haplotype that is identical to "D" in HVS1. "Lineages 10, 14, 42" probably conflates 2, quite possibly 3, different haplotypes.
10-a, 10-c L2a2a, L2a2b, or L2b1  
11, 11-a, 11-c, 11-d, 11-f, 11-g I2a1 The MRCA of all individuals, of all individuals with the I2a1 haplotype, and of all extant branches of family 11 is a sister (1739) to Regulus by the Godolphin Arabian. Hill et al. 2002 reported an atypical haplotype (D1a2) in a single descendant of Young Camilla (1787 Woodpecker), branch mare of 11-b. Bower et al. 2012b does not follow (even though all 100 of Hill’s samples were supposedly included in that study) but did report another atypical haplotype in some of their 11-g samples. Branch 11-g stems from 11-b. These findings indicate two separate errors in the record of Young Camilla’s descendants, neither of which occurred at Young Camilla or her daughter, Mandane (1800 Pot8os), the 11-g branch mare. Possible de novo variants in the expected haplotype have been reported in family 11 (Hill et al. 2002, haplotype "P", Bower et al. 2012b "Lineage 11f").
11-b D1a2  
11-g L2a2a, L2a2b, or L2b1  
12 (descendants of Mother Western) I2a2a The MRCA of all individuals tested is the dam of Mother Western (by Smith's Son of Snake) and a Mare (Sister to Diamond) by Whiteshirt. The findings place different haplotypes under Mother Western, MRCA of all I2a2a individuals, and the Whiteshirt Mare as 3d dam of Sister to Sampson (Greyhound) who is the MRCA of all individuals that did not test I2a2a. This strongly suggests that two different matrilineages were conflated in the final record (GSB1, ed.5) for the early generations of family 12. The atypical (for descendants of Sister to Sampson) A1 haplotype in 12-b indicates an error at or after the 12-b branch mare, imported Diana (1754 Cullen Arabian). The MRCA of all extant 12-b branches is a colonial American mare (1766c by Spotswood’s imported Jack of Diamonds) attributed to Diana's produce only by tradition. Possible de novo variation in the expected haplotype for descendants of Sister to Sampson was reported by Hill et al. 2002 ("Q", Table 1).
See: Deep Rooted Anomalies in Female Families Revealed by mtDNA Testing.
12-b A1b or A1d
12-c, 12-d, 12-f L1a  
13-a, 13-b, 13-c I2a1 The MRCA of all family 13 individuals reported publicly is Rutilia (1769 Blank), the branch mare of 13-a, from which stem 13-b and 13-c. The MRCA of all extant branches of family 13 is Rutilia’s 3d dam, Milbanke’s Black Mare by Makeless.
14-a, 14-b, 14-c, 14-f L2b1 The MRCA of all family 14 samples reported publicly is Boadicea (1807 Alexander). The MRCA of all extant branches of family 14 is her dam Brunette (1790c Amaranthus).
15-a L2b1a The number of family 15-a individuals was variously reported (Bower et al. 2012b) as 6 (Supplemental Information, Table 1) and one (Table 2, main body of report). MRCA is unknown/impossible to determine.
16, 16-a, 16-b, 16-c, 16-f, 16-g, 16-h L3a1b The MRCA of all individuals tested and of all L3a1b individuals is a mare (1823) by Don Juan. The MRCA of all extant branches of family 16 is her 2d dam, Spitfire (1799 Pipator). The MRCA of all individuals tested (Rogers, 2014) from the ‘trunk’ of family 16 is Lady Alice (1855, Chanticleer). The two atypical haplotypes found in two contemporary descendants of one of her daughters probably represent separate errors in the record at or after that daughter since the expected haplotype for family 16 was found in a contemporary descendant another of her daughters. Family 16 individuals with short HVS1 sequences matching the L3a1b haplotype were reported (Bower et al. 2012b) as part of a 3 family conglomerate ("Lineages 2, 8, 16") that conflates two different haplotypes. Subsequent sequencing of family 16 individuals at markers in the coding region identified the typical family 16 haplotype as L3a1b (Rogers, 2014).
16 N2a
16 I2a2a
17-b L3a1a or L3a1a1 MRCA of all individuals tested is unknown. The 17-b branch mare and MRCA of all extant branches of 17-b is Biddy (1829 Bran). The MRCA of all extant branches of family 17 is Worlock’s Galloway (1725 Snake).
18, 18-a A1a MRCA of all individuals tested is unknown. The MRCA of all extant branches of family 18 is [Wyvill's] mare (1725c) by Bartlett’s Childers.
19, 19-b, 19-c H MRCA of all individuals tested, of all that tested “H”, and of all extant branches of family 19 is Tuberose (1772 King Herod), or Sister to Thunderbolt (Woods' Counsellor), if family A15 represents an extension of family 19. The MRCA of all 19-c individuals tested is unknown. The branch mare of 19-c is The Twinkle (1821 Walton). The findings indicate two separate errors in the record after her daughter Cast Steel (1828 Whisker), MRCA of all extant 19-c branches
19-c I2a2a
19-c L2b1a
20, 20-a, 20-c, 20-d I2a2a The MRCA of all individuals tested is unknown. The MRCA of 20-a, 20-c, and 20-d samples is the 20-a branch mare Variety (1808 Hyacinthus). The ‘trunk’ of family 20 is extant in multiple branches between Variety and her 5th dam, a mare (1751) by Cade, the MRCA of all extant branches of family 20. The findings indicate two errors in the final stud book record of one or more of the lines branching from the family 20 ‘trunk’, after the Cade Mare and before Variety.
20 M1a or M2
20 L3a1b or L4a
21-a B1b MRCA of the individuals tested is unknown. The 21-a branch mare is Wagtail (1818 Prime Minister). The MRCA of all extant branches of family 21 is the family taproot, Queen Anne's Moonah Barb Mare (1700c Hampton Court Brown Barb).
22, 22-a, 22-b, 22-d L3a1a or L3a1a1 MRCA of all individuals tested and of all extant branches of family 22 is Canary Bird (1806 Whiskey or Sorcerer).
23, 23-a, 23-b M1a or M2 MRCA of all individuals tested is unknown. MRCA of all extant family 23 branches is Brocklesby (1721 Greyhound). The findings indicate errors in the record after the 23-a branch mare, A-La-Grecque (1763 Regulus) and after imported Gallopade (1828 Catton) the MRCA of all extant branches of 23-b.
The atypical I2a1 haplotype variant reported (Bower et al. 2012b, Table 1, "Lineage 23") in some 23-b individuals disagrees with its corresponding GenBank sequence (EU580167 "TBG-23") which is identical at its length (partial HVS1) with I2a3. I2a3, while unreported in Table 1, is well documented in the TB by sequences from multiple other sources. As shown Bower’s Table 1, "Lineage 23" is identical to and equated with "P" as reported (Hill et al. 2002) in a single individual from family 11 and regarded as a probable de novo variant in the expected I2a1 haplotype for family 11. The "Lineage 23" haplotype may have been mis-reported in their Table 1 by Bower et al. due to clerical mix-up.
23-a B1b  
23-b I2a3 (or I2a1)  
25 N1 The MRCA of individuals tested (Rogers 2014) and of all extant branches of family 25 is Lardella (1780 Young Marske).
26 B1a Single individual reported by Bower et al. 2012b.
42 L2a2a, L2a2b, or L2b1 Bower et al. 2012b reported (Supplemental Information, Table 1) testing 3 individuals from family 42 but only one in the main body of the report (Table 2). Their conglomeration of family 42 with families 10 and 14 probably conflates at least two, quite possibly 3, different haplotypes. See remarks for family 10.
52 L3a1b or L4a Bower et al. 2012b variously reported testing 2 indivduals (Supplemental Information, Table 1) and one (Table 2, main body of the report).
A1 G2a or G2a1 Ballet (1871 Planet) is the MRCA of the individuals with a G2a haplotype (Rogers, 2014). Her 4th dam, Maria West (1827 Marion) is MRCA of all extant A1 branches. Bower et al. 2012b reported finding N2a in a single contemporary individual from A1, lineage unknown. Their conclusion that A1 "derived" from (Lowe) family 1, premature at best to begin with, is most likely wrong.
A1 N2a
A4 N1a MRCA of all individuals tested is unknown. The MRCA of all extant family A4 branches is Fanny Maria by Jackson's Pacolet. The longer mt sequences used by Rogers 2014 prove that contemporary members of family A4 could not, as concluded by Bower et al. 2012b, have "derived" from (Lowe) family 1. The A4 haplotype (N1a) is actually in a different subdivision of haplogroup N than the family 1 haplotype (N2a), closer phylogenetically to the expected haplotype (N1) for family 25. While families A4 and 25 undoubtedly share a recent (in evolutionary context) common ancestral lineage, there is no evidence that they share a dam recent enough to be represented in the historic record.
A29 L1a Bower et al. 2012b variously reported testing 3 individuals (Supplemental Information, Table 1) and 1 individual (Table 2, main body of report).
a48 A1a Single individual reported by Bower et al. 2012b.


References

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Lira J, Linderholm A, Olaria C, Brandström D M. Gilbert M T, Ellegren H, Willerslev E, Lidén K, Arsuaga J L, Götherström A. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Mol Ecol. 2010 Jan;19(1):64-78. Epub 2009 Nov 25.

Lowe, C B, (W. Allison, ed.). Breeding Racehorses by the Figure System. The Field and Queen (Horace Cox) Ltd., UK.

Orlando, L et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499, 74–78 (04 July 2013) doi:10.1038/nature12323

Peng MS, Fan L, Shi NN, Ning T, Yao Y-G, Murphy RW, Wang WZ, Zhang YP. DomeTree: a Canonical Toolkit for Mitochondrial DNA Analyses in Domesticated Animals. Mol Ecol Resour. (2015)DOI: 10.1111/1755-0998.12386

Pruvost M, Bellone R, Benecke N, Sandoval-Castellanos E, Cieslak M, Kuznetsova T, Morales-Muñiz A, O'Connor T, Reissmann M, Hofreiter M, Ludwig A. Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art. PNAS U S A. 2011 Nov 15;108(46):18626-30. Epub 2011 Nov 7.

Rogers, B. Finding Tregonwell’s Natural Barb Mare. Bluebloods. Oct., 2014:30-35.



© J. Baugh 2015

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