Hello,
I am preparing to run an individual-based landscape genetics analysis on Eastern Indigo Snakes and was wondering if someone could provide some guidance on how to deal with individuals identified as full- or half-sibs. My study species is more-or-less continuously distributed across my landscape and I am measuring the genetic distance between samples using Bray-Curtis distances and principle components axes. I understand that researchers often randomly remove all but one member of full-sib families for population genetics analyses but I have seen less justification for this practice in the context of individual-based landscape genetics analyses.
I have tested for the presence of family structure using COLONY v1.2 and v2. They generally give similar results and indicate the presence of one 4-sib family, three 3-sib families, and 15-22 2-sib families (all full-sibs) out of 109 samples. I understand that these small family sizes may suggest that family structure is being poorly estimated and that I should be cautious about inferring family structure from these results. I have other biologically-based reasons to suspect some of these results as well (e.g., unrealistically large distances between some full-sibs).
Nevertheless, I am wondering if there is any utility in removing all but one individual from these full-sib families, even if the family structure is uncertain and if I am conducting an individual-based landscape genetics analysis. I noticed in a 2017 paper by Robin Waples and Eric Anderson in Molecular Ecology where they suggested caution when removing full-sibs in some circumstances, particularly with weak family structure.
Any suggestions would be welcome!
Thank you,
Javan Bauder
Did you check what are the rationales behind the removal of your full/half siblings?
In my experience, there were mainly two reasons (maybe they can be others):
- ensure that your sampling is representative from your whole population. For this, if you can justify your sampling protocol has been well designed, maybe you do not need further checking.
- avoid any violation of hypothesis required for the approach implemented (like HW), but if you need it, I would rather then use the usual tests for this, and decide, based on those results.
Another independant suggestion. You may want to test how your results differ by including or not sibs. If not then you also have your answer.
Dear Javan,
Did you check the consistency of your results across several, independant Colony replicates? When you suspect your molecular information to be low, it is often advised to re-run the analysis with different sampling seeds. You could, for instance, use 5 or 10 replicates and see in which proportions the same families are found.
Also, you could try what happens when performing longer runs or two-three runs instead of one, or by changing the algorithm (for instance, switching from full-likelihood to FPLS). This said, if results are already congruent between Colony v.1.2 and 2, maybe you do not actually need to go that further. I am not familiar with individual-scale landscape analyses though so I'd better not give any more advice in this concern.
Good luck!
Thank you both for your replies and excellent suggestions. My first choice would indeed to try my analyses with and without full-sibs to see if/how the results differ but I might not have the time for that.
Gregoire, my sampling design is very opportunistic (just because Eastern Indigo Snakes are very hard to find) so there is a large cluster of points (about 60% of my samples) within an area roughly one-quarter the size of my entire study area. Some, but not all, of the full-sibs occur within this cluster. But your second point about needing to meet the assumptions of HWE is what I am most wondering about. In my landscape genetics analyses I am testing for a relationship between individual-based genetic distance and cost distance measured on a resistance surface. If genetic distance is measured using only the mathematical dissimilarity among genotypes (e.g., Bray-Curtis distance, Euclidean distance, or principle components axes) then it seems that it does not matter if HWE is met or not (i.e., the assumption of HWE does not seem to come into play in this approach). However, I think I would want a second opinion if this is indeed the case!
Chrystelle, I really like your suggestion about doing multiple runs in COLONY especially with changing the settings.
Thanks again,
Javan
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