What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades

Abstract

BackgroundThe use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals).ResultsWe find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled).ConclusionsOverall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like Plethodon, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses.

Ancient lineage, young troglobites: recent colonization of caves by Nesticella spiders

“…Despite incongruences between the mitochondrial and nuclear gene trees, the concatenated gene tree and the species tree reconstructed with multilocus data strongly supported the same topology separating Nesticella into three geographically well-defined clades: A, B, and C. The combined gene tree was dominated by nuclear data, which was not unexpected since Fisher-Reid and Wiens [49] suggested that nuclear genes had lower levels of homoplasy than mitochondrial genes. The relatively rapidly evolving mitochondrial genes supported the monophyly of Clades A plus B, which probably resulted from ancestral polymorphisms and lineage sorting [49].…”

“…The relatively rapidly evolving mitochondrial genes supported the monophyly of Clades A plus B, which probably resulted from ancestral polymorphisms and lineage sorting [49]. Overall, our data was sufficient to resolve the phylogenetic relationship among the taxa.…”

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

“…In other cases, conflicts with our results might reflect the impact of our sampling fewer nuclear genes and a correspondingly increased influence of mitochondrial data. Mitochondrial genes have relatively fast evolutionary rates (potentially exacerbating the impacts of long branches), and their phylogenetic resolution for a particular node may also reflect introgression or incomplete lineage sorting rather than the species phylogeny (review in [196]). Many taxa in the matrix are represented only by mitochondrial data, and highly variable mitochondrial genes might also overcome the influence of less variable nuclear genes in combined analyses (although this scenario does not seem to be common [196]).…”

Discrete phenotypes are not underpinned by genome-wide genetic differentiation in the squat lobster Munida gregaria (Crustacea: Decapoda: Munididae): a multi-marker study covering the Patagonian shelf

“…Nonetheless, the lack of differentiation at a single marker is insufficient to extrapolate to the entire genome, especially in view of the different inheritance in the mitochondrial and nuclear genomes [74, 75]. A previous molecular study used only mitochondrial evidence and found no consistent genetic differentiation associated with each ecotype [29] but failed to demonstrate genetic homogeneity in the nuclear genome.…”