Data deposited at Dryad: doi: 10.5061/dryad.0453k
Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals
Version of Record online: 10 APR 2014
© 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology
Journal of Evolutionary Biology
Volume 27, Issue 5, pages 899–910, May 2014
How to Cite
Figuet, E., Romiguier, J., Dutheil, J. Y. and Galtier, N. (2014), Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals. Journal of Evolutionary Biology, 27: 899–910. doi: 10.1111/jeb.12361
- Issue online: 28 APR 2014
- Version of Record online: 10 APR 2014
- Manuscript Accepted: 28 FEB 2014
- Manuscript Revised: 27 FEB 2014
- Manuscript Received: 10 FEB 2014
- . Grant Number: ANR-10-BINF-01-02
- European Research Council Advanced. Grant Number: ERC 232971
- 2008. The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies. Mol. Phylogenet. Evol. 48: 964–985. &
- 1998. Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280: 731–734.
- 1983. Mastication and rumination in relation to body size of cattle. J. Dairy Sci. 66: 2137–2141. , &
- 2006. A Bayesian compound stochastic process for modelling non-stationary and non-homogeneous sequence evolution. Mol. Biol. Evol. 23: 2058–2071. &
- 2006. Efficient likelihood computations with nonreversible models of evolution. Syst. Biol. 55: 756–768. &
- 2008. Parallel adaptations to high temperatures in the Archean eon. Nature 456: 942–945. , , , &
- 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43: 610–621. , &
- 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540–552.
- 1988. Cladistic tests of adaptational hypotheses. Cladistics 4: 3–22.
- 1998. Reconstructing ancestral character states: a critical reappraisal. Trends Ecol. Evol. 13: 361–366. , &
- 1981. Population density and body size in mammals. Nature 290: 699–700.
- 1987. Interspecific allometry of population density in mammals and other animals: the independence of body mass and population energy-use. Biol. J. Linn. Soc. 31: 193–246.
- 2009. A database of vertebrate longevity records and their relation to other life-history traits. J. Evol. Biol. 22: 1770–1774. &
- 1989. Phylogenies and the analysis of evolutionary sequences, with examples from seed plants. Evolution 43: 1137–1156.
- 2013. Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons? Genetics 195: 195–204. &
- 2008. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evol. Biol. 8: 255. &
- 2012. Efficient selection of branch-specific models of sequence evolution. Mol. Biol. Evol. 29: 1861–1874. , , , , &
- 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
- 2013. Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution. Prepr. Arxiv1302.5104v1. &
- 1985. Phylogenies and the comparative method. Am. Nat. 125: 1–15.
- 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst. Biol. 55: 301–313. &
- 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283: 220–221. , &
- 2011. Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea. Mol. Biol. Evol. 28: 2661–2674. &
- 2012. Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335: 32–50. , , , , , et al.
- 2005. The evolution of large size: how does Cope's Rule work? Trends Ecol. Evol. 20: 4–6. &
- 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32: 578–601.
- 2006. Ancient polymorphism reveals unidirectional breeding system shifts. Proc. Natl. Acad. Sci. 103: 1359–1363. , &
- 2011. Reducing model complexity of the general Markov model of evolution. Mol. Biol. Evol. 28: 3045–3059. , , &
- 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90: 2648. , , &
- 2010. Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol. Evol. 25: 495–503. , &
- 2013. Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes. Mol. Biol. Evol. 30: 489–502.
- 2012. Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model. Evolution 66: 1773–1787. &
- 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21: 1095–1109. &
- 2011. A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters. Mol. Biol. Evol. 28: 729–744. &
- 2007. Family Anthracotheriidae. In: The Evolution of Artiodactyls (D.R. Prothero, S.E. Foss, eds), pp. 89–105. Johns Hopkins University Press, Baltimore, MD. &
- 2007. The Origins of Genome Architecture. Sinauer Associates Inc., Sunderland, MA.
- 1998. Deleterious mutation accumulation in organelle genomes. Genetica 102–103: 29–39. &
- 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. 90: 4087–4091. &
- 2010. Little evidence for Cope's rule from Bayesian phylogenetic analysis of extant mammals. J. Evol. Biol. 23: 2017–2021. &
- 2008. Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Mol. Biol. Evol. 25: 120–130. , &
- 2013. Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino Acid replacement in mitochondrial genomes of mammals and birds. Genome Biol. Evol. 5: 1273–1290. , &
- 2007. Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc. Natl. Acad. Sci. 104: 20443–20448. , , , , &
- 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54: 397–405. &
- 1987. Very slightly deleterious mutations and the molecular clock. J. Mol. Evol. 26: 1–6.
- 1999. Inferring the historical patterns of biological evolution. Nature 401: 877–884.
- 2007. Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals. Proc. Natl. Acad. Sci. 104: 13390–13395. , , , &
- 2005. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biol. Rev. 80: 445–473. , &
- 2010. Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res. 20: 1001–1009. , , &
- 2012. Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping. PLoS One 7: e33852. , , , , , et al.
- 2013. Genomic evidence for large, long-lived ancestors to placental mammals. Mol. Biol. Evol. 30: 5–13. , , &
- 1982. Skeleton of diacodexis, oldest known artiodactyl. Science 216: 621–623.
- 2009. Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19: 1760–1765. , , &
- 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66: 3931–3944. , &
- 1973. An explanation for Cope's rule. Evolution 27: 1–26.
- 2001. Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature 413: 277–281. , , &
- 2007. Whales originated from aquatic artiodactyls in the Eocene epoch of India. Nature 450: 1190–1194. , , , &
- 2004. Cope's rule, hypercarnivory, and extinction in North American canids. Science 306: 101–104. , &
- 2013. On the origin of cetartiodactyla: comparison of data on evolutionary morphology and molecular biology. J. Paleontol. 47: 321–334.
- 2008. Calculating independent contrasts for the comparative study of substitution rates. J. Theor. Biol. 251: 667–678. &
- 2007. Relationships between body size and abundance in ecology. Trends Ecol. Evol. 22: 323–330. , , &
- 2011. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc. Natl. Acad. Sci. 29: 1861–1874. , , , , &