Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

Abstract

BackgroundThe number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA), two nuclear exons (IRBP and vWF) and four nuclear introns (MGF, PRKC, SPTBN, THY). Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated), we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics.ResultsTaxonomic sampling included multiple representatives of all five rodent suborders described. Fast-evolving positions for each dataset were identified individually using a discrete gamma rate category and sites belonging to the most rapidly evolving eighth gamma category were removed. Phylogenetic tree reconstructions were performed on individual and combined datasets using Parsimony, Bayesian, and partitioned Maximum Likelihood criteria. Removal of fast-evolving positions enhanced the phylogenetic signal to noise ratio but the improvement in resolution was not consistent across different data types. The results suggested that elimination of fastest sites only improved the support for nodes moderately affected by homoplasy (the deepest nodes for introns and more recent nodes for exons and mitochondrial genes).ConclusionThe present study based on eight DNA fragments supports a fully resolved higher level rodent phylogeny with moderate to significant nodal support. Two inter-suprafamilial associations emerged. The first comprised a monophyletic assemblage containing the Anomaluromorpha (Anomaluridae + Pedetidae) + Myomorpha (Muridae + Dipodidae) as sister clade to the Castorimorpha (Castoridae + Geomyoidea). The second suprafamilial clustering identified a novel association between the Sciuromorpha (Gliridae + (Sciuridae + Aplodontidae)) and the Hystricomorpha (Ctenodactylidae + Hystricognathi) which together represents the earliest dichotomy among Rodentia. Molecular time estimates using a relaxed Bayesian molecular clock dates the appearance of the five suborders nearly contemporaniously at the KT boundary and this is congruent with suggestions of an early explosion of rodent diversity. Based on these newly proposed phylogenetic relationships, the evolution of the zygomasseteric pattern that has been used for a long time in rodent systematics is evaluated.

Chromosomal evolution in Rodentia

“…The monophyly of anomaluromorphs was recently confirmed by DNA sequences (Montgelard et al, 2008;Blanga-Kanfi et al, 2009). Nine extant species are currently recognized in the suborder.…”

Bony labyrinth morphometry indicates locomotor adaptations in the squirrel-related clade (Rodentia, Mammalia)

“…The squirrel-related clade is characterized by different types of locomotion [31,32] and comprises the families Sciuridae, Aplodontidae and Gliridae [33][34][35][36]. The relationship between these three families is contradictory and subject of many morphological (e.g.…”

Fossil and molecular evidence constrain scenarios for the early evolutionary and biogeographic history of hystricognathous rodents

“…Some have argued that phiomorphs and caviomorphs are likely to have shared a common Afro-Arabian ancestor (15)(16)(17), while others have suggested that the phiomorph-caviomorph split might have occurred in Asia, and that caviomorphs dispersed to South America either through Afro-Arabia or via a southern Gondwanan route (13,18). One critical issue that has hindered understanding of the group's historical biogeography is the phylogenetic position of the family Hystricidae, which has been placed as either the sister group of a phiomorph-caviomorph clade or as the sister group of Caviomorpha, in recent molecular phylogenetic analyses (9,(19)(20)(21). Temporal and tectonic constraints on competing biogeographic hypotheses have also been limited by radically different molecular estimates of the phiomorph-caviomorph split, which range in age from Ϸ85 Ma to Ϸ36 Ma (9,18,19,22,23).…”