Abstract
One of the fundamental assumptions in the multi-locus approach to phylogeographic studies is that unlinked loci have independent genealogies. For this reason, congruence among gene trees from unlinked loci is normally interpreted as support for the existence of external forces that may have concordantly shaped the topology of multiple gene trees. However, it is also important to address and quantify the possibility that gene trees within a given species are all inherently constrained to some degree by their shared organismal pedigree, and thus in this strict sense are not entirely independent. Here we demonstrate by computer simulations that gene trees from a shared pedigree tend to display higher topological concordance than do gene trees from independent pedigrees with the same demographic parameters, but we also show that these constraining effects are normally minor in comparison to the much higher degree of topological concordance that can routinely emerge from external phylogeographic shaping forces. The topology-constraining effect of a shared pedigree decreases as effective population size increases, and becomes almost negligible in a random mating population of more than 1,000 individuals. Moreover, statistical detection of the pedigree effect requires a relatively large number of unlinked loci that far exceed what is typically used in current phylogeographic studies. Thus, with the possible exception of extremely small populations, multiple unlinked genes within a pedigree can indeed be assumed, for most practical purposes, to have independent genealogical histories.
Highlights
Lineage sorting and gene coalescence are inherently rather stochastic processes, so genealogies of physically unlinked genes within a sexually reproducing species are expected to exhibit considerable topological incongruence unless external forces somehow act on populations to shape multiple gene trees concordantly
Multiple gene trees sampled from a single organismal pedigree might show a higher level of topological concordance than gene trees sampled from independent pedigrees with
Under all levels of gamete dispersal, gene trees sampled from the same organismal pedigree consistently showed a significantly higher level of genealogical concordance (C) than did gene trees sampled from independent pedigrees (Fig. 3)
Summary
Lineage sorting and gene coalescence are inherently rather stochastic processes, so genealogies of physically unlinked genes within a sexually reproducing species are expected to exhibit considerable topological incongruence unless external forces somehow act on populations to shape multiple gene trees concordantly. There are 2G possible gender-defined transmission routes for autosomal alleles traced back through G generations, but only four of them (FfiFfiFfiFfi ...; FfiMfiFfiMfi ...; MfiFfiMfiFfi ...; and MfiMfiMfiMfi ...; where F and M are males and females) are completely non-coincident in every generation (Wollenberg and Avise 1998) Based on this observation, it seems at least theoretically possible that the underlying organismal pedigree could materially constrain the distribution of gene tree topologies even in the absence of other external forces. Multiple gene trees sampled from a single organismal pedigree might show a higher level of topological concordance than gene trees sampled from independent pedigrees with
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