Variance of molecular datings, evolution of rodents and the phylogenetic affinities between Ctenodactylidae and Hystricognathi

Abstract

The von Willebrand factor (vWF) gene has been used to understand the origin and timing of Rodentia evolution in the context of placental phylogeny. vWF exon 28 sequences of 15 rodent families and eight non-rodent eutherian clades are analysed with two di¡erent molecular dating methods (uniform clock on a linearized tree; quartet dating). Three main conclusions are drawn from the study of this nuclear exon. First, Ctenodactylidae (gundis) and Hystricognathi (e.g. porcupines, guinea-pigs, chinchillas) robustly cluster together in a newly recognized clade, named`Ctenohystrica'. The Sciurognathi monophyly is subsequently rejected. Pedetidae (springhares) is an independent and early diverging rodent lineage, suggesting a convergent evolution of the multiserial enamel of rodent incisors. Second, molecular date estimates are here more in£uenced by accuracy and choice of the palaeontological temporal references used to calibrate the molecular clock than by either characters analysed (nucleotides versus amino acids) or species sampling. The caviomorph radiation at 31 million years (Myr) and the pig^porpoise split at 63 Myr appear to be reciprocally compatible dates. Third, during the radiation of Rodentia, at least three lineages (Gliridae, Sciuroidea and Ctenohystrica) emerged close to the Cretaceous^Tertiary boundary, and their common ancestor separated from other placental orders in the Late Cretaceous.

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.…”

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

“…Because changes in evolutionary rate are widespread, a ''global'' clock tree cannot always be easily obtained by the removal of fast-or slow-evolving taxa without sacrificing taxon sampling (Takezaki et al 1995;Huchon et al 2000;Murphy et al 2001b). This is the reason a so-called local molecular clock approach was recently proposed by Yoder and Yang (2000).…”

“…However, the most confounding and widespread cause is likely to be the variation of evolutionary rates, precluding the use of the global molecular clock concept (Zuckerkandl and Pauling 1965). In eukaryotic genes, lineage-specific substitution rate variations have been documented for protists (Philippe and Germot 2000), plants (Bousquet et al 1992), fungi (Moncalvo et al 2000), and various animals such as insects (Huelsenbeck 1998), cyclostomes (Mallatt and Sullivan 1998), and mammals (Huchon et al 2000). Rate variations have also been detected for mitochondrial genomes among mammals (Gissi et al 2000).…”

“…Two mammalian orders have long been the subject of intensive studies regarding their evolutionary rates: rodents and primates. For some molecular markers, rodents have been shown to evolve more rapidly than other placentals (Wu and Li 1985;Adkins et al 2001) and to display within-order rate heterogeneities (Huchon et al 2000). Primates are also characterized by different rates of molecular evolution between lineages, namely, faster rates in anthropoids (Adkins and Honeycutt 1994;Andrews et al 1998;Andrews and Easteal 2000;Liu et al 2001).…”

From the Cover: Protein sequence signatures support the African clade of mammals

“…Several authors have used the concept of such ''sequence signatures'' qualitatively in molecular phylogeny (e.g., refs. [15][16][17][18][19], but thorough statistical interpretations are lacking.…”