For these birds, isolation-by-distance is (almost) all in the family

A Florida scrub jay (Flickr: Candace Martino)

Isolation by distance is one of the most fundamental processes of molecular ecology. In any finite population, the frequency of a genetic variant will change from generation to generation due to random sampling effects, which we call genetic drift. In two separate populations a genetic variant can drift to different frequencies — but migration between the two can keep them “synchronized.” Across a larger landscape, if migration becomes more difficult between more distant pairs of populations, this isolation, by distance, can allow them to evolve measurable genetic differences.

This process is important for molecular ecologists because we study the genetic differences between populations, and IBD creates those differences as a simple consequence of time and space. If you don’t take IBD into account, you can mistake its results for local adaptation, which is the very thing we’re most often interested in — genetic differences between populations that reflect adaptation to different environments.

As important as IBD is, though, we don’t usually study it directly. Instead, we test for its consequences, by comparing genetic differences between pairs of populations at different distances, to see whether genetic differences increase with geographic distance. To see how migration across a landscape creates those genetic differences, we’d have to track the movement of multiple generations of individuals across a region — no trivial task. Precisely that kind of data, though, has just been released as a preprint on bioRxiv.

In the preprint, Stephanie Aguillon and her coauthors examine a population of Florida scrub-jays, which are ideally suited for studying IBD. Young adult jays remain in their parents’ breeding territory for up to six years, helping to support un-fledged siblings and patrol for predators. Scrub-jay pairs defend their home territories year-round, and young jays can set up on their own by inheriting their parents’ territory, carving out a new territory from their parents’ territory, or finding unoccupied habitat elsewhere. Biologists at the Archbold Biological Station have been observing one population of Florida scrub-jays for decades, tracking hundreds of birds in a tract of oak scrub habitat small enough to cross in a brisk afternoon hike.

Knowing the dispersal history and the family histories of all these birds, the collaborators could then collect genetic samples and compare differences in DNA sequence to those relationships to reveal how individual birds’ ancestry combines to form a population-wide pattern of IBD.

(A) Female scrub jays (orange bars) disperse farther from the nest where they’re born, on average, than male scrub jays (blue bars). (B) In the Archbold Station population, this creates a north-south pattern of population genetic differentiation across different jay families’ breeding territories. (C) And it means that genetic similarity of pairs of male jays (blue line) starts higher and drops off faster with distance than female-male pairs (purple) or female-female pairs (orange). (Aguillon et al.: Figure 1)

The first big pattern is a sex bias. Male jays are much more likely to inherit some or all of their parents’ territory, so, on average, breeding males are found closer to where they were born. Half of the males tracked in the Archbold population established territories within less than 500 meters of their parents’ territory; for females, the equivalent distance is more than a kilometer. The genetic data — about 8,000 single-nucleotide polymorphisms, genotyped in every adult jay in the population in three different years spaced across the longer-term study period — reflect these short dispersal distances, and the sex bias. Detectable genetic differences are visible from one end of the Archbold population to the other, a distance of about 10 kilometers (6 miles).

The sex bias is apparent in comparisons of genetic differences between pairs of individual jays with breeding territories at different distances: male-male pairs from adjacent territories are much more genetically similar than male-female pairs or female-female pairs at the same distance; at distances greater than one kilometer, these differences disappear. (The study’s authors express genetic difference in terms of “identity by descent,” which is the probability that two individuals share a stretch of DNA sequence that they inherited from a common ancestor. One of the great annoyances of population genetics is that two key concepts are abbreviated as ‘IBD.’ I’ll stick to using it for isolation-by-distance.)

Those curves of declining genetic similarity can be summarized in terms of the distance at which similarity declines halfway from its maximum (between individuals in adjacent territories) to its “background” level. For male-male pairs, this “delta” term is 620 meters; for female-female pairs, it’s 903 meters. Perhaps counterintuitively, that lower “delta” term indicates stronger isolation-by-distance, because it means the genetic similarity of male-male pairs decreases faster — and, thus, genetic differences between male-male pairs increase faster — with distance.

Isolation-by-distance becomes less pronounced as related individuals are removed from the dataset. The “r” statistic measures familial relatedness; full siblings have r = 0.5, while r = 0.03125 corresponds to second cousins. (Aguillon et al.: Figure 3B)

The known pedigree relationships of the Archbold scrub-jays let the authors identify how IBD is created by familial history. Successively removing comparisons between individuals with more and more distant relationships depresses the pattern of IBD in the dataset — parent-offspring and full-sibling pairs contribute a big chunk, grandparent-grandchild, half-sibling, and aunt/uncle-niece/nephew (or “nibling”) pairs contribute another. But even removing all pairs of individuals that were at least second cousins left a significant relationship between geographic distance and genetic differences.

For the full dataset, the “delta” statistic measuring the effect of IBD is about 600 meters; with all pairs that are at least second cousins removed, delta increases to about one and a half kilometers. That lower-level IBD that isn’t explainable by the known family histories of the Archbold scrub-jays probably reflects a history that goes back before Archbold Biological Station was established. In other species — those that migrate longer distances over the course of their lives, or live longer — more of IBD is in this category, a deep population genetic structure we can only attribute to the isolating effect of distance, without knowing the individual histories that built it.

References

McGowan KJ, GE Woolfenden. 1989. A sentinel system in the Florida scrub jay. Animal Behavior. 37:1000-1006. doi: 10.1016/0003-3472(89)90144-9

McGowan KJ, GE Woolfenden. 1990. Contributions to fledgling feeding in the Florida scrub jay. Journal of Animal Ecology. 59(2): 691-707. doi: 10.2307/4889

Aguillon S, JW Fitzpatrick, R Bowman, SJ Schoech, AG Clark, G Coop, N Chen. 2016. Deconstructing isolation-by-distance: the genomic consequences of limited dispersal. bioRxiv, doi: 10.1101/093989

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About Jeremy Yoder

Jeremy Yoder is an Assistant Professor of Biology at California State University, Northridge. He also blogs at Denim and Tweed, and tweets under the handle @jbyoder.

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