Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. This talk describes a detailed literature survey of mitochondrial DNA studies on low-level insect phylogeny and phylogeography, results from which reveal the frequency of non-monophyly and patterns of interpretation and sampling. Our findings show species-level paraphyly and polyphyly to be unexpectedly common and call for increased attention to sampling and the interpretation of complex gene trees.
Keywords: gene trees, mitochondrial DNA
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