female families

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stancaris
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female families

Postby stancaris » Mon Dec 26, 2011 11:36 am

To all: If I look up the pedigree of a horse and find it traces in tail female to Fritzette can I be reasonably sure that Fritizette is in tail female of that horse. A few years ago a study was done that found errors in the original studbook which means that certain families were wrong. Could it be that the horse I find on pedigree query.com that traces to Fritzette in tail female really doesn't trace to her at all?

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Pan Zareta
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Re: female families

Postby Pan Zareta » Mon Dec 26, 2011 12:14 pm

stancaris wrote:To all: If I look up the pedigree of a horse and find it traces in tail female to Fritzette can I be reasonably sure that Fritizette is in tail female of that horse. A few years ago a study was done that found errors in the original studbook which means that certain families were wrong. Could it be that the horse I find on pedigree query.com that traces to Fritzette in tail female really doesn't trace to her at all?


I can't find a Fritzette or Fritziette. If you're referring to FRIZETTE 1905 x Hamburg, ff 13-c, no published studies to date that correlate mtDNA haplotype with lineage or family number have reported anomaly in family 13.

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Re: female families

Postby parlo » Sat Dec 31, 2011 12:20 pm

Pan Zareta wrote:... no published studies to date that correlate mtDNA haplotype with lineage or family number have reported anomaly in family 13.


This is not quite true: Hill et al. discovered and pointed out, that "the mares at the head of [Bruce-Low-] families 4, 11, 13 ... derived from a single common founder, and this was perhaps not surprising, given that the three were all owned by James D'Arcy and kept at the same stud at aboud the same time." (quoted from Binns/Morris: Thoroughbred Genetics, London 2010)

That says: the "foundation mares" of families 4, 11, 13 might be sisters or at least had a common ancestor in direct tail-female-line. Would this common ancestor have been identified, 3 families would merge into a single common family.

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Pan Zareta
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Re: female families

Postby Pan Zareta » Sat Dec 31, 2011 2:32 pm

parlo wrote:This is not quite true: Hill et al. discovered and pointed out, that "the mares at the head of [Bruce-Low-] families 4, 11, 13 ... derived from a single common founder, and this was perhaps not surprising, given that the three were all owned by James D'Arcy and kept at the same stud at aboud the same time." (quoted from Binns/Morris: Thoroughbred Genetics, London 2010)

That says: the "foundation mares" of families 4, 11, 13 might be sisters or at least had a common ancestor in direct tail-female-line. Would this common ancestor have been identified, 3 families would merge into a single common family.


Parlo, yes the founder haplotype of those families are the same so they are part of the same large equine mitochondrial DNA family (and it's one which encompasses more breeds/types than just the TB). But the mutation rate of mtDNA is measured in thousands of years and those families may not all share an ancestor in tail female within the last 5000-10,000 years, much less one recent enough to be called "founder" or "foundation mare". People far more familiar with the evidence from the historic record than Ms. Hill believe the evidence favors a shared a 17th cent. founder for families 11 & 13. The evidence re. family 4 is more equivocal.

The report from the study by Hill et al. was published 2002, and must be regarded within the context of subsequent equine mtDNA studies and reports. What I've read suggests that the conclusion, 2002, that a "web of founder-sharing" had been uncovered was grossly premature.

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Postby parlo » Mon Jan 02, 2012 9:46 am

The report from the study by Hill et al. was published 2002, and must be regarded within the context of subsequent equine mtDNA studies and reports. What I've read suggests that the conclusion, 2002, that a "web of founder-sharing" had been uncovered was grossly premature.


@PZ: Thanks. Would be kind to share your resources with us if there have been scientific evidence on that matter more recently than 2002.

... But the mutation rate of mtDNA is measured in thousands of years and those families may not all share an ancestor in tail female within the last 5000-10,000 years


This shall be correct in a strictly scientic view. But remember: in Britain there has been breeding of so-called "running horses" before the year 1680. Those mares in the Royal Stud and similar old studs should have been selected and should have own racing- and breeding-records with many relatives among them. Many of those mares should be "foundation mares" of "our" thoroughbreds - even if we don't know their pedigrees and can't identify them from early stud books.

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Postby Pan Zareta » Mon Jan 02, 2012 12:42 pm

parlo wrote:@PZ: Thanks. Would be kind to share your resources with us if there have been scientific evidence on that matter more recently than 2002.

For purposes of defining the TB haplotypes represented Table 2 p. 290 of the 2002 report by Hill et al. two "insertion/deletion event" (indels) were ignored (see p. 289). One of those deletions (at nucleotide position 15528) has since been recognized as a valid point of segregation between haplotypes (see McGahern et al. 2006). Had it been recognized as such in 2002 at least two haplotypes would have been apparent within what was then regarded as one, "F", which was deemed representative of founder in families 2, 7, 8, 16, 17 & 22. While there is no specific reference to those families in the 2010 report by Bower et al. the distinction is reflected in definitions of GenBank TB d-loop sequences associated with that report and with an as yet unpublished report entitled Thoroughbred mitochondrial DNA reveals closer than expected links between maternal genetic history and pedigree records .

Additionally, in 2006 Harrison & Turrion-Gomez reported that mtDNA haplotype could not always be fully defined from d-loop alone. Based on my own observations of GenBank mtDNA sequences from all breeds I'd say that there is one particular haplogroup in which some haplotypes certainly cannot be fully defined from the segments of d-loop used for either their study or that by Hill et al. 2002, and that while analysis of d-loop outside those sequences can offer more precise resolution, analysis of the polymorphisms in the coding region is probably necessary for greatest confidence. Both haplotypes represented by "F" (Hill et al. 2002) are in this particular haplogroup. I don't think the possibility for further refinement within "F" can be ruled out.

Evidence from GenBank sequences also suggests the possibility of further refinement within haplotype "H" (Hill et al. 2002). There are TB d-loop sequences there associated with other studies that are identical to "H" within the d-loop segment used for the 2002 study but which segregate outside of it.

When mtDNA began to be marketed as a tool for the researcher of human genealogies it quickly became apparent that within many, maybe most, haplogroups analysis of markers in the coding region was required for definitions precise enough to be of any meaningful use. Equine mtDNA probably doesn't have quite the same level of diversity as human mtDNA, but it's no surprise at all that adequate haplotype definition should be more complex than was believed nearly 10 years ago.

This shall be correct in a strictly scientic view. But remember: in Britain there has been breeding of so-called "running horses" before the year 1680. Those mares in the Royal Stud and similar old studs should have been selected and should have own racing- and breeding-records with many relatives among them. Many of those mares should be "foundation mares" of "our" thoroughbreds - even if we don't know their pedigrees and can't identify them from early stud books.


Your point is well taken. I agree that there are undoubtedly shared recent common ancestors among founder mares who are unconnected by stud book record. The point I'm trying to make is that if mtDNA is to provide reliable evidence in this regard the haplotype definitions need to be as precise as possible.

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Postby parlo » Mon Jan 02, 2012 2:08 pm

Thank you VERY MUCH!

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Postby vineyridge » Mon Jan 02, 2012 6:07 pm

PZ, you are a treasure.
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