Why direct offspring counts miss a breeding line’s reach
Research note · Breeding-line records
Abstract
Counting an animal’s direct offspring tells us how often it appears as a parent in a set of records. It does not tell us how far that animal’s line extends through later recorded generations. We measured both in a published 237-dog research pedigree. One founder, PFZ13D08, appears as a parent of 13 sampled dogs and as an ancestor of 123 unique sampled descendants. Another, PFZ24C06, appears as a sire of 41 sampled dogs—the highest direct count in this file—but has 55 unique recorded descendants. The three most frequently recorded sires account for 91 of 212 sire links. These are properties of the sampled pedigree, not breed-wide breeding rates, genomic contribution, or a time trend.
Two different questions about a line
A direct offspring count asks: how many sampled dogs name this animal as a parent? A descendant count asks: how many sampled dogs can be reached by following recorded parent–offspring links through any number of generations? The second includes the first, but the two counts can diverge sharply. A dog with fewer direct offspring may sit earlier in a well-represented branch and have many more descendants in the available file.
That distinction matters when a parentage record is corrected. The edited animal’s direct offspring are the first records to inspect. More distant descendants may also need review, especially if the correction changes ancestry shared by a previously checked pairing. Descendant reach identifies records downstream of a link; it does not say that every downstream Match result changes.
Data and method
We used the six pedigree fields in new_pedigree_dogs.fam from the data released with Campbell et al. (2016). The paper describes 237 DNA samples from a Labrador Retriever–Greyhound research colony. The file has 212 recorded sire links and 207 recorded dam links: 207 sampled dogs have both parents recorded, five have one, and 25 have neither. These are sampled records, not a census of every dog born in the colony.
For each sample ID, we counted distinct direct offspring named in its parent fields. We then followed the parent–offspring graph through all later recorded generations and counted each reachable descendant once, even if more than one pedigree path connects the same two animals. We checked parent references, sex codes, and cycles. An independent traversal from parents to children reproduced all 237 direct and descendant counts in the derived table.
Sire-link concentration uses a different denominator: each of the 212 sampled dogs with a recorded sire contributes one sire assignment. Offspring from the same sire–dam pair are separate records here, but they are not independent mating decisions. The file has no birth or registration dates in these fields, so we cannot order the assignments over time.
Results: direct count versus recorded reach
| Published sample ID | Direct offspring | Unique recorded descendants |
|---|---|---|
| PFZ13D08 | 13 | 123 |
| PFZ27D02 | 7 | 117 |
| PFZ26F05 | 28 | 103 |
| PFZ24C06 | 41 | 55 |
All four are founders in the available file, meaning their own parents are unrecorded here. PFZ24C06 has the most direct offspring of any sampled animal, yet PFZ13D08 reaches more than twice as many unique sampled descendants. The counts answer different questions; 123 descendants are not 123 equal genetic contributions, and the descendant totals for different ancestors overlap.
Recorded sire assignments are also concentrated within this sampled colony. Eighteen distinct sires appear across the 212 sire links. The three with the highest counts are:
| Recorded sire | Sampled offspring naming him as sire |
|---|---|
| PFZ24C06 | 41 |
| PFZ26F05 | 28 |
| PFZ24E05 | 22 |
| Top three combined | 91 of 212 (42.9%) |
The concentration is a descriptive count of this research file. It is not evidence of a breed-wide “popular sire” pattern, a measure of effective population size, or a claim that any of these animals was overused in a wider population. The per-animal results include all 237 sample IDs, including animals with no recorded descendants.
What a changing record calls for
Direct offspring and unique descendants provide two useful scopes for reviewing a changed parent link. The direct children are closest to the correction. The descendant set shows how far that link could propagate through the recorded family graph. To learn whether a particular pairing’s coefficient changes, we still have to recompute that pairing with the verified parentage. Our separate one-link sensitivity study did exactly that: among 419 single-link omissions in this same pedigree, 19 changed at least one of 30 fixed pairing calculations.
For AnimalTrace, the practical question is which records a breeder, lab, or registry should inspect after new evidence arrives. Search and saved updates help locate the changed record; the family relationships define the records to follow; Match evaluates the specific pair again. A descendant count is a useful way to scope review, not a substitute for source verification or a pair-specific calculation. Our worked Search and Match example uses a smaller family from this public dataset.
Limits and reproducibility
The source is a selected set of 237 DNA samples from one research colony. Dogs outside the file, unrecorded parents, and later offspring cannot appear in these counts. The descendant measure records reachability through stated parent links; it does not estimate a descendant’s fraction of inherited DNA, health risk, or breeding value. We analyzed no genotype calls or clinical outcomes. Without dates, a static concentration cannot establish an increase, decrease, or other trend. No population sampling design supports a statistical inference to a breed or registry.
- Source study: Campbell et al., 2016, A Pedigree-Based Map of Recombination in the Domestic Dog Genome.
- Source data: Authors’ public repository,
new_pedigree_dogs.faminsidedog_genotype_data.tar.gz. - Derived data: Direct offspring and unique recorded descendants for all 237 samples.
- Method: Download the standard-library Python script to reproduce the counts from the public
.famfile.
This AnimalTrace research note has not undergone external peer review.