Are the Heteromyidae paraphyletic? Molecular phylogenetics of extant geomyoid rodents

Abstract

The superfamily Geomyoidea includes the Geomyidae (pocket gophers: 7 genera, 42 species) and Heteromyidae (pocket mice, kangaroo mice, and kangaroo rats: 5 genera, 69 species).  Analyses of both morphological and molecular data have confirmed the monophyly of the superfamily relative to other rodents but have cast doubts on the reciprocal monophyly of Geomyidae and Heteromyidae.  The latter are recovered as paraphyletic in some, but not all molecular phylogenies, with low to moderate support for critical nodes.  To test alternative hypotheses of geomyoid phylogenetic relationships, we searched NCBI databases and assembled four datasets: a) the 13 protein-coding mitochondrial DNA genes (7 genera, 13 species); b) the mitochondrial 12s, 16s, and COX1 loci (7 genera, 43 species); and two datasets of ultraconserved elements (UCEs; 6 genera, 9 species): c) one with 3,991 loci, allowing for up to 2 unrepresented taxa per locus, and d) another one reduced to 1,750 UCEs (with no missing data).  In all cases, beavers were included as outgroups.  Maximum likelihood analysis of both mitochondrial datasets were equivocal regarding heteromyid paraphyly, as support for the critical nodes was very low.  In contrast, the trees obtained from UCE loci with both Maximum Likelihood and a multi-species coalescent method (wASTRAL) indicated that pocket gophers were sister to pocket mice (100 % bootstrap, local Posterior Probability of 1), to the exclusion of kangaroo rats, which formed a second, strongly supported clade (100 % bootstrap, local Posterior Probability of 1; Figure 3).  These preliminary findings are consistent with the hypothesis that Heteromyidae are paraphyletic relative to Geomyidae.  The inclusion of additional taxa (e. g., kangaroo mice) in the analyses is required to confirm these results.