Primate phylogeny, evolutionary rate variations, and divergence times: A contribution from the nuclear gene IRBP

Abstract

The first third (ca. 1200 bp) of exon 1 of the nuclear gene encoding the interstitial retinoid-binding protein (IRBP) has been sequenced for 12 representative primates belonging to Lemuriformes, Lorisiformes, Tarsiiformes, Platyrrhini, and Catarrhini, and combined with available data (13 other primates, 11 nonprimate placentals, and 2 marsupials). Phylogenetic analyses using maximum likelihood on nucleotides and amino acids robustly support the monophyly of primates, Strepsirrhini, Lemuriformes, Lorisiformes, Anthropoidea, Catarrhini, and Platyrrhini. It is interesting to note that 1) Tarsiidae grouped with Anthropoidea, and the support for this node depends on the molecular characters considered; 2) Cheirogaleidae grouped within Lemuriformes; and 3) Daubentonia was the sister group of all other Lemuriformes. Study of the IRBP evolutionary rate shows a high heterogeneity within placentals and also within primates. Maximum likelihood local molecular clocks were assigned to three clades displaying significantly contrasted evolutionary rates. Paenungulata were shown to evolve 2.5-3 times faster than Perissodactyla and Lemuriformes. Six independent calibration points were used to estimate splitting ages of the main primate clades, and their compatibility was evaluated. Divergence ages were obtained for the following crown groups: 13.8-14.2 MY for Lorisiformes, 26.5-27.2 MY for Lemuroidea, 39.6-40.7 MY for Lemuriformes, 45.4-46.7 MY for Strepsirrhini, and 56.7-58.4 MY for Haplorrhini. The incompatibility between some paleontological and molecular estimates may reflect the incompleteness of the placental fossil record, and/or indicate that the variable IRBP evolutionary rates are not fully accommodated by local molecular clocks.

Test of the Optimal Body Size Model for Strepsirhines

“…strepsirhines, includes numerous regions of the genome, and supports many of the phylogenetic relationships reported from morphological studies. We supplemented the phylogeny with more recent genetic data (Delpero et al, 2001;Mayor et al, 2004;Poux and Douzery, 2004;Wyner et al, 2000;Yoder et al, 2000). Serial independence tests indicated significant phylogenetic autocorrelation for male body size (C = .442, p = .001) and female body size (C = .685, p = .001), but not for 2-dimensional home range size in males (C = .169, p = .197) and females (C = .201, p = .171).…”

Deep evolutionary roots of strepsirrhine primate labyrinthine morphology

“…The molecular phylogeny of extant strepsirrhines is well documented (Yoder et al 1996(Yoder et al , 2000Yoder, 1997;Pastorini et al 2001Pastorini et al , 2002Pastorini et al , 2003Poux & Douzery, 2004;Roos et al 2004;Yoder & Yang, 2004). Furthermore, adaptive radiation within each major strepsirrhine group led to a wide spectrum of locomotor specializations (Martin, 1972;Rasmussen & Nekaris, 1998) such that extant strepsirrhine diversity represents an ideal testbed to assess functional vs. phylogenetic factors influencing the morphology of the bony labyrinth.…”

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

“…Divergence dates estimated with a constant rate of molecular change among all lineages are likely complicated by such rate heterogeneity. Local molecular clocks have been used to control for the rate variations to date primate divergences (35,48), but the heterogeneity within catarrhine primates (i.e., the hominoid slowdown) has not yet been incorporated into analyses specifically to estimate the hominoidcercopithecoid divergence.…”