Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents.

Yuri Kimura,Melissa T R Hawkins,Molly M Mcdonough,Lawrence J Flynn,Louis L Jacobs

doi:10.1038/srep14444

Abstract

Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.

Highlights

Divergence time estimates in phylogenetic studies have become increasingly valuable for addressing questions regarding lineage diversification rates, evolutionary patterns, and historical biogeography, among others[1,2]
Accepting the transition from Antemus to Progonomys as a calibration point for the Phloeomys/core Murinae split is entirely dependent on molecular tree topology, and direct morphological evidence has not been demonstrated in the fossil record
We have shown that diverging tooth morphology in the Siwalik lineages was initiated by 11.2 Ma, with decreasing morphological overlap through time[34] between the Progonomys and Karnimata clades (Fig. 1C), and that the 11.2 Ma stratigraphic occurrence can be considered as the evidence of lineage separation under the initial split criterion[36]

Summary

Introduction

Divergence time estimates in phylogenetic studies have become increasingly valuable for addressing questions regarding lineage diversification rates, evolutionary patterns, and historical biogeography, among others[1,2]. Molecular phylogenetic studies have clarified evolutionary relationships of the Murinae and confirmed that the earliest split within the subfamily is the divergence between the Phloeomyini and core Murinae, followed by the Mus/Rattus split within core Murinae[9,22,23,24,25,26,27,28,29,30] As a result, this 12 Ma fossil-based date is more commonly assigned to the Phloeomys/core Murinae split[9,24,26,27,29,30,31]. The rationale for considering the first appearance of Progonomys as the Mus/Rattus split is based on the simplified phylogenetic hypothesis of Siwalik murine rodents by Jacobs[33] and Jacobs and Downs[10], which proposed dichotomous lineages (the Progonomys clade and the Karnimata clade), deriving from Antemus (Fig. 1A, see SI Discussion for details). No further morphological evidence is found for the evolutionary relationship between Rattus and Siwalik species of the Karnimata clade[35]

Methods

Results

Conclusion