@ARTICLE{TreeBASE2Ref18691, author = {Jonathan M. Waters and Diane L. Rowe and Chris P Burridge and Graham P. Wallis}, title = {Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation.}, year = {2010}, keywords = {}, doi = {10.1093/sysbio/syq031}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {59}, number = {5}, pages = {504--517}, abstract = {Mechanisms of speciation are best understood in the context of phylogenetic relationships, and as such have often been inferred from single gene trees, typically those derived from mtDNA markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g. due to stochastic lineage sorting, introgression, or selection). Here we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from Galaxias brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on three independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here we use pseudogene (galaxiid Numt: 1801 bp), intron (S7: 903 bp) and exon (RAG-1: 1427 bp) markers, together with mtDNA, to re-evaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp), and concatenated nuclear and mtDNA (4770 bp), both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus Bayesian analysis (BEST) that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA.} }

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