SNPs Resolve the Phylogenetic History of Chinese Geckos Where mtDNA and Morphology can Mislead

Discordance between mitochondrial DNA (mtDNA) trees and species history is not uncommon and caused by several well‐known processes. Differences in phylogenetic signal between loci within the mtDNA genome have received less attention. Large amounts of nuclear genomic data provide the opportunity to resolve uncertain phylogenetic inference in cases of discordance. We examined relationships among three putative divergent lineages of Chinese webbed‐toed gecko: Gekko subpalmatus , G. cib (formerly G. subpalmatus ) and G. melli . MtDNA sequences ( ND2 / COXI ) were analyzed and an mtDNA tree that supported (( G. melli and G. subpalmatus ) and G. cib ) was obtained. This differed from a recent well‐supported mtDNA–based phylogeny. To resolve this, we estimated species trees using genomic SNPs (from genotyping‐by‐sequencing), which supported our ND2 / COXI tree. We investigated how the mtDNA loci used in these studies might provide discordant phylogenetic signals by comparison of 16 trees obtained from individual mtDNA loci. Well‐supported trees, but with two distinct topologies, were obtained for six of the loci, while the remaining 10 loci provided weakly‐supported topologies. Only three mtDNA loci provided a well‐supported tree that was concordant with the genomic SNPs tree. This suggests that differences in phylogenetic signal across the mitochondrial genome misled previous phylogenetic inference. Divergence time dating revealed quite similar internal node ages, which likely exacerbated this effect. Finally, we analyzed generalized divergence in body dimensions: the two nonsister taxa G. subpalmatus and G. cib were the least divergent lineage pair, potentially explaining previous incorrect conclusions. We conclude that different well‐supported phylogenetic histories can be supported by different mtDNA loci while large numbers of genomic SNPs provide more reliable topologies.