Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations

Abstract

Abstract. Reconstructing the chronology of mammalian evolution is a debated issue between moleculeand fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.

Accelerated Rate of Gene Gain and Loss in Primates

“…These divergence times are broadly consistent with other estimates (Adkins et al 2003;Douzery et al 2003;Steppan et al 2004). Divergence times for human, chimpanzee, and macaque were taken from other studies (Nei and Glazko 2002;Kumar et al 2005;Patterson et al 2006), as both chimpanzee and macaque were not included in the Springer et al study.…”

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid–cercopithecoid divergence

“…The divergence date for the hominoid-cercopithecoid split is estimated by using a maximum likelihood-based quartet analysis (49), a method that has found widespread taxonomic utility in calculating divergence times (33,(49)(50)(51)(52)(53)(54)(55)(56). Here this method is expanded to large genomic contigs sequenced in catarrhine primates.…”

“…Within mammals there is considerable evidence for evolutionary rate heterogeneity, with different mammal groups evolving at different rates (28)(29)(30)(31)(32)(33)(34)(35)(36)(37), although this finding has been questioned (38). While some studies run contrary to this finding (39,40), there is also considerable evidence for rate heterogeneity within primates, particularly that hominoids are evolving slower than cercopithecoids (the ''hominoid slowdown'') (15,32,34,(41)(42)(43)(44)(45)(46)(47).…”

A widespread problem: cryptic diversity in the Libyan jird

“…The model with the highest likelihood was run for 1 × 10 9 iterations (sampling every 1 × 10 5 with 10% burn-in samples removed). The molecular clock was calibrated using the fossil-dated split between Mus and Rattus of 16 million years ago (mya; normal distribution, SD = 1.5) as calculated by an averaging approach across multiple calibration points (Douzery et al 2003). Due to the low reliability of the fossil record within Gerbillinae, no additional internal calibration point could be used in our analysis (Tong 1989).…”