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I am conducting a phylogeography study of a fish species and am trying to construct a phylogenetic tree to describe population structure and ancestry. I have constructed trees using various measures of genetic distance, such as Nei's DA, DS, and Edwards Chord distance. The answers I get between these measures are conflicting, but each explained by a sound hypothesis, and so I must carefully and objectively choose which measure of genetic distance is to be most trusted given my data. So my question to the community is not, "which should I choose?" but "how should I choose?" I am interested in an answer or (ideally) resource that describes what factors I should take into account and that may bias my result.

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  • $\begingroup$ Just curious, but is there a reason why you didn't mention/aren't concerned with Centimorgans? I only ask because I'm uneducated in phylogenetics, but when I was studying genetics (in university), that was the unit we used to measure relative chromosomal "distances". $\endgroup$ – Charles Aug 8 '17 at 19:40
  • $\begingroup$ I think we are at cross purposes: cenimorgans describe the statistical distance (linkage) of markers from one another on one genome. What I am interested in is the distance in terms of divergence between multiple genomes (population samples) for the same marker or set of markers. $\endgroup$ – Robert Aug 8 '17 at 20:49
  • $\begingroup$ Yes, I remember we were studying linkage analysis at the time of that unit being introduced. Makes complete sense! $\endgroup$ – Charles Aug 8 '17 at 20:51
  • $\begingroup$ Have you looked at Rogers, Deriving Phylogenetic Trees from Allele Frequencies: A Comparison of Nine Genetic Distances? $\endgroup$ – mgkrebbs Oct 1 '18 at 3:53

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